Pashute Yid, Chafets Chaim brings at the end of the “Ahavas Chesed” a list of hanhagos of R. Molin. One of them is the shita you mentioned. However, it is clear from the sefer “Chafets Chaim”, that he did not agree with this shita.
In many simonim in the Shulchan Aruch there are halochos about reshoim. None of the commentaries there say that all these halochos do not apply nowdays. Most Poskim do not hold of this far-off shvere kula. According to this shita, all the kofrim, murderers, noafim, thieves etc. can not be treated as reshoim. This is very shvere.