A couple of ideas;
- a mod that removes all options to pay a bounty with the guards once the bounty exceeds 999 gold, so murder is not payable. This would keep the thieves guild option to pay intact, as I can see that working more lore-wise.
- an optional, harsher add on that makes prison matter more. When resting at a prison bed, you are given a dialogue option perhaps, asking you how you will pass the time. Depending on how you answer your stats are reduced, in addition to what the prison bed normally does.
"Meditation" has the game randomly pick health or stamina to be reduced by 10, preserving Magicka.
"Exercise" has the game randomly pick health or magicka to be reduced by 10, preserving Stamina.
"Rest" has the game randomly pick stamina or magicka to be reduced by 10, preserving Health.
I think the changes would motivate players to not break the law, and not get caught doing it if they do. Even breaking out of prison becomes worthwhile. The 1000 gold limit applies to whether being a Thane can get you out of trouble, so I feel it makes sense for murder to not be payable either.
I don't have the expertise or wherewithal to make such an overhaul, but if someone else does and likes the idea(s), I would be grateful and wish you luck.