The reward in not using your amnesty isn't a competitive reward so much as it is fiscal. Paying Gilbert Arenas $22M (per year!) is punishment enough as far as i'm concerned even if it doesn't count against them.
Additionally Boston isn't a large market so we can't pull a Knicks/Lakers/Nets and just dole out $100M in salary. Most teams can't as those teams seem to be the exceptions.
Anyway I agree amnesty is not exactly fair but I'm not sure that there is a good way to make it fair. It's an executive mulligan and really unless you change (raise) the cap for teams that don't use their amnesty I don't see how you can equalize...oh wait I just pitched a solution
I also think their should be less restriction on when it can be used. That would make it more likely to be used by more teams. One week over the summer is too restrictive in my opinion.
Being fiscally responsible is it's own reward, specifically from an owner's standpoint and especially in smaller media markets. Amnesty allows for more parity (making less pitifully bad teams) and if you didn't need to use it you probably weren't pitifully bad, at least at decision making.