After admission, should I thank a recommender who I suspect wrote a bad letter?
Yes, you should thank and inform your letter writer, and no, you shouldn't worry about some bizarre and unrealistic "re-evaluation" of your admission.

Comments: It is very unlikely that your writer wrote a negative letter. In general, one only agrees to write a letter if one has something constructive or positive to say. Having read lots of letters, I'll note that even judgmental and perfectionist people put their criticisms in context, comparing to their general assessments of other students or researchers. (I.e. this person isn't perfect, but he/she is better than most others for the following reasons). These letters, in fact, are often the most compelling. 

As a further comment, you're being very uncharitable in assuming bad intentions of someone who agreed to write a letter for you! 

And a final comment: no university is going to care to "re-evaluate" their admission of you, even in the stunningly unlikely event that someone asks them to, except in cases of actual fraud, criminal issues, etc. Everyone involved has better things to be doing with their time.