Yitayningwut: I don’t see how else you can explain the Mishnah in Pirkei Avos. The Mishna is discussing pure character; not behavior or actions.
There are many things which the Torah permits, but it is nevertheless proper to try to refrain from doing; like Gezel Achu”m (midoraysa), capital punishment (for Beth Din), Bi’ah Shelo Kidarka, Go’el Hadam etc. So, even though the Torah permits Shechita on a regular basis it still may be considered proper to refrain from eating animals [at least during weekdays when it’s not a mitzvah at all].