I'm thinking that there is not a way to do this (perhaps with some programming and maybe not even then).
There's too much variation in the cleanup, like:
What if the suppressed feature is aligned to another feature and they share connecting centerlines?
SW would have to also hide that connector(s)?
What if the suppressed hole was connected between two other holes?
SW would have to know to remove the center mark and the two connection lines and then replace these with one connection line to fix the original alignment?
What if a dimension referenced the center mark of a suppressed hole but there was an aligned hole beyond that needed that dim?
SW would have to know to remove the center mark, the connection line and then associate the dim to the remaining hole's mark and maintain/fix the dim's text placement.
I don't think center marks (and their connection lines) have enough inherent intelligence for this.
Be nice if they did.
(P.S.: It's getting to be that time of the year, maybe if you write a letter to SolidWorks Claus...;)
Yeah I guess that makes sense. Thanks for the explanation.