I dont know MegaSync, but i cannot believe that there is NO option to define, which folders have to by synched and which not. So you can only synch the whole PC (even if it has a 10 TeraByte Disk??)? Strange.
P.S.: When i enter "exclude folders from megasync" into Google, it gives me tons of useful hints. Of course you can define folder names, which should not be synched (thats perfectly designed, simply apply "tmp" and ALL temporary folders will be skipped, exactly what you need). Already one of the top level answers in Google gives me this link:
https://github.com/meganz/MEGAsync/issues/55 - a quote from there:
At the moment you can define exclusions in Advanced/Settings.
Why cant you find that?