Profootballtalk.com's take:
"Also, even though the league seemingly legitimized the whole poison-pill thing by attempting to strike a deal with the union that would have removed it from the CBA, there's no guarantee that the device will be upheld the next time a case involving it ends up in arbitration. Last year, the Seahawks inexplicably abandoned their arguments on the merits of the matter and showed up at the hearing claiming that, because they had pushed around some of the money in left tackle Walter Jones' contract, Steve Hutchinson would have been the highest paid offensive lineman on the team, and thus Seattle could match the offer sheet that Hutchinson had signed in Minnesota without the deal being fully guaranteed.
What if this time around the Fins had opted to argue that, even though the poison-pill does not require a team to pay more money by matching, the device as a practical matter entails more money because it eliminates the team's inherent ability to terminate the deal early? And what if the arbitrator had decided that the poison-pill is a form-over-substance device that violates the spirit of the CBA?
Bottom line -- the Pats avoided a bunch of potential worries and headaches for a throwaway pick in the bottom of the draft."
http://www.profootballtalk.com/rumormill.htm
Very good point. Perhaps the Patriots legal team decided that there was a significant chance this wouldn't hold up, or at least it would take a long time to resolve. This may have had nothing to do with not looking like scum, just good management.