There sort of is a way to use mods permanently, though I would only recommend it with very non-intrusive changes. You can directly modify the core game files with your mod, which will not only allow it to be run without the mod interface but also allows you to gain achievements playing with your mod. The biggest downside is that the game will revert all such changes every time it updates from Steam. About the only "mod" I have made this way is changing the max XP from barbs from 30 to 60, but you could theoretically make any changes a mod can do in this way. Modify core game files at your own risk. Also, make sure everyone playing a multiplayer match with you has made the same changes, or unexpected things may occur.
Is this how the high score tables were broken? Essentially hacking the game?