I've had this exact thought in the past, but nobody will let me modify the code to change it.
Thanks system I believe is an addon, not an official with this version of vB. So it would be somewhat flaky making them work together. The problem is that reputation is governed by spreading out, so if they were linked together effectively you would either block a thanks from being added, or you would create a thanks with no reputation alteration.
I like the reputation system since I use it to govern the usergroups. Fortunately, all that matters is that users give negative rep to users that are *just* short of breaking the rules, but you'll know they'll be back to modify spam in :P. Negative rep prevents them from moving into the confirmed group where they get the signatures, the moderation filtering removed, and the ability to edit.
header('HTTP/1.1 420 Enhance Your Calm');