The nice thing about the $100 fee is that if and when you do decide to go AEA, the $100 comes off of your initiation fee.
I don't know much about the Chicago theatre scene, but when I was EMC I never felt like it was stopping me from working at smaller theatres. But, as babens says, no reason you have to let non-AEA companies know about it, if you're worried.
Another pro is that you don't actually need 50 weeks to go AEA, you just need someone to offer you an AEA contract. So if you are EMC, and you reach a point where you want to be AEA and have been offered an AEA contract, and you don't have the weeks yet, you can join regardless.