I am looking for a tool that will convert my mkv file to an mp4 file, but is devoid of malware and bloatware.
FFMpeg It's a command line program but it can convert a MKV to a MP4 without recompressing the file. Very quick.
The command to do so would be
ffmpeg -i input.mkv -c copy -c:s mov_text output.mp4
If you do some further digging, you can probably find a script to help. Actually, you might look at this Apple.StackExchange answer.