I don't see a problem playing both guys.
You don't just hand the job to a guy, you want one to earn it. With the three trades for middle infielders this season, any one of them could get the job at 2b. Bonifacio needs experience, and he's getting that. He's playing and getting AB's, but stting and still putting in work at the big league level still helps him out.
He is the best bet to be the answer at 2B on opening day next year, but there's no guarantee long term. Danny Espinosa, Smiley Gonzalez, and Jake Smolinski have just as much of a case to stake as the future at 2b(if Espinosa plays SS, then Smiley is a 2B, and vice versa).