If it does, then your funds should be relatively safe, as there is nothing a thief can do without your 2fa codes. However, if it doesn't, and you just have a standard wallet, there is a chance that the malicious version could contain a keylogger and have sent your wallet file/seed/password to the hacker.
In any case, the fact that you downloaded, installed and ran a "malicious" version of Electrum means that it could have been laced with any number of viruses/malware such as Remote Access Trojans (aka RATs), keyloggers, screengrabbers etc...
Unless you do either a full system sweep using AV/Antimalware software or, preferably, a full system wipe and reinstall, then you can't really be confident that your system is "OK". Whether or not you're comfortable with that risk is up to you.