Does that lead to the conclusion that the penalties and punishments (whether enforced by Beis Din Shel Maata or by the Beis Din Shel Maala) that the Torah specifies for various sins done by Jews will be inapplicable in that era?
The Gemara in Zevachim 55a – discussing the disqualification of Piggul in Korbonos – asks “הלכתא למשיחא”, seemingly bothered by the fact that we discuss halachos that are only relevant after the coming of Moshiach. (There are numerous difficulties with this gemara; I just want to bring out one point:) Tosfos lists numerous places where the Gemara clearly does not have this issue, and a couple of places where the Gemara does.
One of Tosfos’ tirutzim is that the Gemara only raises this issue when discussing Halachic conclusion of issues that are only relevant with the fulfillment of two criterion: (a) after the coming of Moshiach (b) through a Jew sinning.
The Tosfos Yeshanim and the Ritva both explain this by adding שאז יהיו כל ישראל צדיקים – in that period, sin will be obsolete, and therefore these Halachos will never be relevant again. (Tos. in Yuma write similarly to what they write in Zevachim, although the wording there is clear that this isn’t their intention.)
If I remember correctly, Tos. discusses Misas Bes Din as one of his examples.