Paulie was certainly sweating bullets in "Remember When" on that boat with Tony. He kept seeing images of he and the guys whacking Puss while on the boat. While Paulie was for the most part a stand-up guy, I could also see times when Tony and/or Junior would have had him clipped.

Tony also would have had a real justification to whack Paulie after Paulie & Chris let that Russian guy slip away in Pine Barrens.

I always thought the writers would have brought that Russian back in one of the last episodes in attempt to exact revenge.