I'm afraid I don't know of any papers that discuss indispensability and impure set theory directly. In a sense there's a reason to think that impure set theory is nice to have for physics. As you know, it's natural to represent functions in set theory as sets of ordered pairs, hence if you want to talk about functions that map spacetime points to other spacetime points, you'll need impure sets (if those functions don't float your boat, pick your favourite physical objects that you want to talk about functions from/to).
However, to say that impure set theory is indispensable is a much stronger claim. It's also going to be tough to establish, given (as I'm sure you're aware) that the universe(s) of pure sets is pretty big, far bigger than the physical universe (on any plausible theory of the physical universe; the biggest I think you can reasonably get it is if you allow mereological sums of spacetime points then you might be able to argue for the universe having cardinality $2^{2^{\aleph_0}}$, which is diddly squat in set theoretic terms). Given then the sheer abundance of sets, we can always represent new an interesting physical phenomena by pure sets, in such a way that the impure set theory is dispensable.
However, one should be mindful of the dialectic into which an indispensability argument is often inserted. Usually there is some sort of Quinean holism in the background providing the necessary oomph to think that indispensability to science matters. Given this, one's question really should not be "what is indispensable to science?", but rather, "what is indispensable to our best theory of the world?".
If the latter is the question, and if one thinks that categoricity is important for a mathematical theory (say for worries about first-order theories being unable to pin down their intended model up to isomorphism), one might be interested in the following paper by McGee:
McGee, Vann; `How We Learn Mathematical Language', The Philosophical Review Vol. 106, No. 1 (Jan., 1997), pp. 35-68
There he gives a full categoricity proof for $ZFC$ (on the assumption of unrestricted first-order quantification), by first adding urelemente and proving the categoricity of the pure sets from the impure universe. Thus if it turned out that urelemente were indispensable for this task, one might think that that impure set theory is an indispensable part of our best theory of the world after all.
[As a footnote, it should be noted that there are plenty of other ways to get categoricity given unrestricted first-order quantification. See, for example:
Martin, Donald A. (2001). Multiple universes of sets and indeterminate truth values. Topoi 20 (1)
who argues that any two universes of sets (satisfying certain criteria) can be combined,
and
McGee, Vann (1992) Two Problems with Tarski's Theory of Consequence Proceedings of the Aristotelian Society New Series, Vol. 92, (1992), pp. 273-292
where he argues for categoricity through the introduction of a satisfaction predicate.]
s(p,t)
may be glossed as a vector which gives the position of a particle p at a time t.