I do agree that some sort of better/more obvious warning for going over fuel or supply limits would be nice. Doesn't need to literally stop play and bring up a window, but should at least magnify/highlight the tiny red tooltip showing player being over some limit.
But as for salvaging and getting too much fuel or cargo in general... player can always just dump cargo pods and stabilize their orbit (or don't if it's just a little cargo, go waste supplies exploring rest of system and then come back after). The primary issue is the cargo pod stabilization cost, which I guess has a bug in it or just needed balancing, since patch notes (or maybe it was a Twitter post?) list reducing/flattening the growth curve for when a player is stabilizing cargo pods. Plus, player has to go pick up the cargo pods eventually (roughly 1 cycle, IIRC), but in practice so long as the pods were stabilized, you can sometimes get lucky and still pick them up 2 or 3 cycles later (just sucks remembering where since no map notes function in vanilla, so have to remember where you left stuff, or tediously search each system map and hopefully get lucky, or get that notes mod).
I am a little unclear if unstabilized pods actually despawn following some random period of time after player has left system with the dumped pods, or only after drifting off of the system map (since NPC fleets seem to mostly ignore the pods, few times I've seen them "steal" pods it seem related to some mod interaction, maybe Nex?). But only really relevant if you are too cheap/poor/lazy to stabilize pods...
So since average player can (and should) just dump excess cargo and fuel (stabilized or not), seems like making the system self righting would just punish newbs... can't have that!