AA really only had two options; to take the five year deal and work until he got fired, or choose not to take the deal at all.
Taking the deal with the idea that you can opt-out is a nightmare scenario. Two possible outcomes:
1) You have a great to decent season and you Opt out. Makes you look greedy and disloyal.
2) You have a crap season. Your stock as GM is a ton of notches below where it is now.
If AA didn't like Shapiro, then what he did was the only choice. Whether that choice is selfish, smart, dumb, disloyal, egotistical, forward thinking, etc. is subjective, and really only AA's inner circle knows the truth.
Upon reflection, he was an alright GM. I think he did more good than bad, but it's pretty 50/50. His run the last year was remarkable albeit short-sighted. I get that sometimes you gotta go for it, and for a city that's staved of that type of excitement I was game. I'll miss the 'wtf' moments from AA, but I do look forward to Shapiro's philosophy, even if it will take some pain for gain.