The official White House position is that it is good that Menendez stepped down as Foreign Relations chair but that it's his own decision whether to resign from the Senate. Why?
This is the right stance, imo. He was duly elected for a six-year-term. A mere indictment does not require a resignation.
But leaving aside the merits, Rs are unlikely to get behind Menendez being removed, so if you are Biden, why do you burn all bridges by calling for his resignation? Especially when Menendez could just become a lobbyist in a worst-case scenario after going to jail.
Even if menendez is eventually redeemed why would Biden care that he would become a lobbyist years after biden is both out office, and presumably passed away? This is not the sort of thing you can walk away from.
The only reason biden isn't kicking him is that Joe has a tragic case of Senate Brain, which means the longer you spend in the chamber the more you are tricked by its own propaganda (worlds greatest debating chamber and so on).