Having a story where he contemplates ending it, but then decides to own up (after appropriate talks with some mentors - Geordi and Data), comes clean to Picard, and then is still kicked out, showing real consequences, leading him to pursue other things
Journeys End could have stayed the same, but without Wesley's sullen responses to Geordi and Data. As Wesley would no longer be a cadet, and being the only person on the ship who could talk to Picard honestly (as Guinan was clearly off ship at the time)
Skip all that nonsense about Picard's ancestors, put in a genuine Picard internal conflict between doing the right thing in preventing relocation, and doing the right thing to prevent war. Maybe you even have Guinan argue against war, taking the "needs of the many" side.
Then at the end everything breaks down and Wesley still goes off with the Traveler
Make Picard's choice clearer, but have him explicitly choose needs of the many on his own back - not hiding behind orders. Then in Insurrection he can see how he regretted it, all he did was delay the war, leading to even more deaths, and pushing Cardassia into the hands of the Dominion, and that explains why he's back on the "no relocation" side.
If there were any alternate timelines (other than Parallels which branched before Wesley went to the academy, and he likely just got field promoted to Lieutenant) they could examine Wesley living with guilt of the coverup