I doubt your primer would bond to a wall with silicone. I'm no wallcovering expert but I do know what the specifications usually call for. I bet there will be someone here with an answer. Maybe even more than 1.
The problem now is going to be fixing it. How much area did this?
I have never heard of any magical solution to fix these things other than what you mentioned, cutting each bubble or using a hypodermic needle to squirt some glue into the bubble then try and roll it down with a seam roller or maybe even a smoother.
Hope it works out for you.