So, if studies prove that a particular kind of isotopes are in rocks originated at the end of the Ordovician, we need to assume that Earth was hit by a flood of elements during that period.
You what? 
How the hell is a supernova going to result in a measurable difference in the concentration of heavy elements?
It doesn't.
...Well, technically there's a thing called photoneutron process which means that if a neutron is hit by a gamma ray with energy higher than the binding energy, it can be ejected from the nucleus, causing the isotope to become
lighter (which can cause it to become unstable and further decay into other isotopes). There are definitely sufficiently energetic gamma rays in gamma bursts, to achieve this, but the question is would it cause detectable changes. Which is a three-fold question; first is the rate of transmutation achieved by the gamma burst, second is the stability of the isotopes made, and the third is the rarity of the isotopes in question.
If the rate of transmutation is small enough (too small amount of nuclei go through the isotopic changes), they can't be detected.
If the half-lifes of the isotopes are small enough, there's no chance to detect the rare isotopes after hundreds of millions of years.
If the isotopes happen to be common, there is really no way to tell what caused them.
All in all, I don't think there is any way to detect if such event took place based on the isotopes, similar to how asteroid or comet impacts can be detected. To introduce alien isotopes on Earth in any detectable or meaningful volume (detectable amount) requires an actual influx of the isotope (impact of some sort, which you referred to with the indium traces), or a neutron flux of significant strength... And there's no way in heaven or hell that either the heavy elements from the supernova or the neutron flux from it would ever reach Earth through several light years of space.
Nearby gamma burst would have other effects, mainly on molecular level, which could possibly be detected. Stuff like changes in crystal structures of some minerals for example... I'm going to just quote wikipedia because I don't think there's much I can add or improve on this:
A gamma-ray burst in the Milky Way, if close enough to Earth and beamed towards it, could have significant effects on the biosphere. The absorption of radiation in the atmosphere would cause photodissociation of nitrogen, generating nitric oxide that would act as a catalyst to destroy ozone. According to a 2004 study, a GRB at a distance of about a kiloparsec could destroy up to half of Earth's ozone layer; the direct UV irradiation from the burst combined with additional solar UV radiation passing through the diminished ozone layer could then have potentially significant impacts on the food chain and potentially trigger a mass extinction. The authors estimate that one such burst is expected per billion years, and hypothesize that the Ordovician-Silurian extinction event could have been the result of such a burst.
So, yeah. I don't think isotopic concentration of soil layers from different times can be used to detect gamma bursts in any meaningful accuracy. I could be wrong though, but there just seems to be too many problems with it.