Although this discussion has moved on quite a bit, I’ll try to attempt a few answers to the initial questions. I am not a philosopher, so you’ll have to bear with me using a more colloquial than technical language, and some of this may sound obvious or has already implicitly been said, but here goes.

First, I’ll rephrase the questions as following: Why is scientism used as a pejorative term, what metaphysical position is this pejorative term aimed at and what reasonable arguments can be made against this metaphysical position?

Why is ‘scientism’ used as a pejorative term?

First, scientism is used as a pejorative term because it was coined as such. It started out as a criticism of someone else’s metaphysical position, not describing someone’s own. Second, from a psychological point of view it is not surprising that a metaphysical position that is asserted by some of its proponents in a way to fundamentally challenge and exclude any other metaphysical position can be perceived as a provocation and cause an emotional response. So can these other metaphysical positions, this alone should not be enough to justify the use of a pejorative term.

What metaphysical position is this pejorative term aimed at?

It has been argued here that the metaphysical position in question is that scientific method is the only possible way of reaching certainty. One argumentation that has been made for it, as far as I understand it, is that all metaphysical positions are accidental, but one happens to coincide with objective reality. For evolutionary reasons, someone was bound to accidentally come up with a metaphysical position coinciding with objective reality, and someone is bound to accidentally adopt it. This metaphysical position could probably be called physicalist, so there would be no need to use the term scientism in either a pejorative or defiant way.
However, as far as I can see the use of the term scientism is often not aimed at a particular metaphysical position itself but rather at statements and conclusions based on it, as well as supposed motivations for adopting it. So the point in question isn’t whether any metaphysical position is more valuable or factually true than another. While the criticism does often seem to be partly caused by an emotional response, as the use of a pejorative indicates, that does not necessarily mean it is unjustified.
So I would propose that both the reason for the use of a pejorative, and the difference between scientism and, for example, physicalism, is that the former designates a metaphysical position and the latter designates invalid conclusions or rationalizations reached through holding this metaphysical position. To answer the question in the thread title, scientism is not a particular metaphysical position but a particular set of actions based on a particular metaphysical position.

What reasonable arguments can be made against this metaphysical position?

The arguments I am aware of either criticize statements and conclusions based on it from a methodological point of view, or motivations for adopting it from a psychological point of view.

From a methodological point of view, the line dividing physicalism from scientism would be crossed once the metaphysical position interferes with scientific convention. I here postulate scientific convention to be right from a functional point of view because it has shown to lead to fairly accurate predictions and consistent results within its field. For example, scientific convention proposes X cannot be proved or disproved by scientific methods, period. Physicalism proposes X cannot be proved or disproved by scientific methods, therefore it does not exist. It is however not the metaphysical position that is scientism here, but the refusal to suspend it in favour of scientific practice, just as any theist would need to suspend his metaphysical position in favour of scientific practice.
A common criticism against scientism is that it declares whole areas of empirical experience as illusory and whole areas of knowledge as irrelevant on the grounds that they cannot be proved or disproved by scientific methods. It is a nice twist that it thereby also declares its own metaphysical position to be illusory or irrelevant on the same grounds, which either accidentally or intentionally makes it unassailable. This may be one reason why physicalism is prone to scientism, as it assumes either that metaphysical positions do not influence the results of scientific experiment and are therefore irrelevant, or that since its own metaphysical position accidentally coincides with objective reality it therefore does not interfere, so in either case it does not need to be scrutinized.
While a metaphysical position does not change the scientific facts, it might determine what scientific facts are found and how they are interpreted by influencing the formulation of the theory, the choice of method, the set-up of the experiment, the interpretation of the data and so on. But even supposing all scientific facts can be found regardless of or unaffected by the assumed metaphysical position, then it does not follow why any metaphysical position should be given up, either scientism, or for example theism. As long as everybody sticks to scientific method, a diversity of metaphysical positions might only get the job done sooner, which in turn would confirm the practical usefulness of metaphysical positions other than physicalism.

From a psychological point of view, it would depend on how important a belief in the validity of science is to the structure of an individual’s personality. The line dividing science from scientism would be crossed once a refutation of the universal and exclusive validity of science is perceived as a threat to one’s own psychical integrity. In this case it would serve the function of an ersatz religion. It turns the fundamental uncertainties shown by science – that we cannot fully trust our senses, that we cannot fully control our actions – into metaphysical certainties – that we cannot trust our senses at all, that we cannot control our actions at all, except through scientific method. Paradoxically, uncertainty and reserving judgment are the very virtues of scientific method.
That certainty might be a psychological need could be explained on biological terms, for example that it is necessary to survival to be certain a given plant is edible. To presume scientism is adopted as an ersatz religion does not contradict its own assumption that the adoption of metaphysical positions is accidental and biologically determined. If the motivation for adopting scientism is a psychological need for certainty or inability to tolerate uncertainty, then maybe this explains why it is associated with materialist metaphysical positions. In practice, theist scientists seem to be more comfortable in keeping science and belief separate than atheist scientists. Maybe this is because, supposing metaphysical certainty is a psychological need, then religion satisfies this need for religious scientists, while atheist scientists expect science to satisfy it.