How much easier would it have been for everyone if Anon had just aimed for Clu, instead of going for Clu's disc there aboard the Regulator?

I mean, sure - nice shot . Ten out of ten for style, but minus several million for good thinking, yeah?

Well, if he'd aimed at Clu, then the main bad guy in Tron Legacy would have been killed /before/ the movie, and that would have totally ruined the story. But from a practical standpoint, yeah, he should have aimed at Clu.

I must list spoiler warning for anyone, just out of consideration but here goes...

In sneak attacks like that, time is of the -immediate- essence, not accuracy.

Anon may have also had a directive protocol to save any ISO left*. Plus the thoughts on Kevin is Clu could've lead to it as well.

We do know in the movie Quorra said Reintegration was the only surefire way...but entiher Kevin nor Clu would survive....this thought does indeed imply Clu dying equals the end of Kevin.

* - This protocol could have been installed into Anon when Flynn found Anon before that scene.