Your first question is kind of a pointless retrospective question. Sure, now that we know that overflow can be a problem in this way, we should consider transactions that attempt to overflow to be suspicious.
The bug was detected by inspection of the blockchain. The bad transactions stood out. Had it not been detected by inspection, sooner or later it would have been detected by the presence of too many Bitcoins circulating.
There are no issues any more. Each individual output is now checked in a way that ensures that their sum cannot exceed the input to the transaction. Overflow is, so far as we know, no longer possible.
Your question seems to be asking if there's some "magic bullet" that can solve similar future problems that are presently unknown. The thing is, if there was, we wouldn't know it because we don't know what the future problems are likely to be. Sure, in retrospect, there are many things that could have been differently that would have made this particular exploit impossile.