Hello Kyle!
I don't think I have much experience here, also because after I complete two lengths of complicated tracks I try to avoid tracks altogether for a long time...
But I have seen stuff like this, and so I say you might go the easy way or the hard way... The easy way might be filing the pins down a little, to make them shorter and less prone to crushing. The track might get pretty fragile after something like that.
OR you might drill the holes out and use catual pins made of wire. I know, a lot of holes to drill, it's a chore... But tank modellers sometimes HAVE to do that.
Anyhow, good luck with your build and have a nice day
Paweł