The money thing kind of rapidly becomes a non-issue later in the game, but even during the story as long as you still have other things to buy you can just drain off cash on those needed SDUs and items first. Mildly annoying but you kind of need to buy them anyway so whatever.
What I do hate is having to redo the entire tree to move a couple of points to something else, or when I accidentally take an extra point in something and have to start over. You should be able to remove points from activated skills as long as it doesn’t block out something lower in the tree for a cost so they can be placed somewhere else. In practice this means having to jot down current skill allocations on paper or screenshot them in case you want to go back. Either way is clunky enough that it just ended up limiting the number of options I’ll bother to try out very heavily, and I think is part of what drives so many people to copy builds from youtube videos / other sources rather than mess around with the trees on their own. This is one of my only real complaints about the borderlands series TBH.