So, I just want a simple tweak that'll change the way owned beds work ingame. It's really frustrating accidentally getting a bounty just from clicking on owned beds. I'd much prefer if the message that said you can't sleep in an owned bed appeared with an okay box so that you got the message, but you got no bounty, much like how it works in Skyrim and Oblivion.

Is there a mod that does just that, if not, can someone make one, or tell me how I can make one?

I would use such a mod.

i think you need to remove ownership from the beds mostly. then editing the script to prompt about ownership, etc. the only issue is that you lose the ability to sleep in an owned bed if you break the line of sight or kill the owner. though i suppose you can still script for that, just that it'd be a hefty script.

The one I know is Jacoby's Ownership Indicator updated for MGE-XE by Hrnchamd, it does not work with beds only though.
http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=9184

I looked at this a bit. If the player is unobserved an owned bed can be used without a bounty. If observed the player will receive the message that it is illegal to sleep in another's bed and may receive a bounty. The latter appears to depend upon the observer's level of alarm.

I do not see an elegant way of managing this with a mod. One could detect if the player received a bounty upon activating an owned bed and then reduce the player's bounty, but the message that the player's crime has been reported will still display ruining the effect.

This appears to be hard-coded and therefore the best solution would need to be through the Morrowind Code Patch. It is not really a bug, but I have noticed that the code patch has broadened its mission parameters to include such tweaks.

Ownership is not something that can be modded, even with the Code Patch....iirc.

But the Ownership Indicator is at least a good way to work-around the problem.