Update: I seem to have found a way to re-enable blacklisted extensions, though I'd guess that eventually it'll automatically get disabled again and I'll have to repeat the process.
Close Opera and go to your user folder (On windows: "C:\Users[username]\AppData\Roaming"), then Opera Software, Opera Stable, and open "Preferences" in a text editor that has a find feature. Look for your extension's ID (for Tampermonkey, it's "dhdgffkkebhmkfjojejmpbldmpobfkfo"), and look for the entries ("blacklist":true,"blacklist_state":1) next to it. Change "true" to "false", and "1" to "0". Save the file and launch Opera - the extension should be enabled now.