Sounds like a clutch problem to me. I've never had a manual Merc but I assume its a hydraulic clutch like my Supra and when that started failing the clutch felt like poo and wouldn't disengage properly. I also had this problem when a clutch fell apart on a truck.

You probably didn't do anything horrible to the trans but you did take some life out of the synchros. I'd fix the cause which is likely a clutch or shift linkage problem, change the fluid, and drive it.

Edit: to be specific my issue was the slave cylinder was leaking.

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Current fleet:
1995 C36
1989 190E 2.6 5 speed
1974 450SLC
1988 5.0 swapped Supra