*Is it possible to have a penalty for spamming but remain in the index and have PR intact?*

Quite possible, from what I see far fewer sites get banned/PR0ed these days, they just suffer from mysterious drops.

Not sure simply deleting those pages will do much for you, you may need a fine comb, an apology (with explanation) showing true remorse, and a promise of future good behaviour.

Otherwise known as a re-inclusion request as IH mentions...