Is there a way to get an installed RPM's signature Key ID programatically?
To answer the actual question, no, there is no way to directly query for the keyid. I ran into the same problem you're having and found someone actually created a bug report with redhat for a feature to request that feature be added.
In the bug report, the responder says to use something like below:
rpm -q --qf "%|DSAHEADER?{%{DSAHEADER:pgpsig}}:{%|RSAHEADER?{%{RSAHEADER:pgpsig}}:{(none}|}| %{NVRA}\n" emacs | cut -d' ' -f11
Any reason you can't clip the relevant portion of SIGPGP with cut? I strongly suspect it's located at the same offset in every rpm header, but you should probably check RPMs from multiple sources just to be sure.