I'm not sure where you are getting your numbers?
According to Fangraphs, when Bogaerts played 3B in 2014, his DRS was -7 and his UZR/150 was -29.4. His dWAR that year was -4.8, though that included his play at shortstop as well.
Marrero's DRS this year is +1, his UZR/150 is +22.4, and his dWAR is 4.0.
As far as catering to Bogaerts' happiness, my personal opinion is that a player should do whatever is best for the team, and if that means moving to a different position, then the player should do so willingly. However, we've tried moving Bogaerts to 3B before and it did not go well. In this case, I don't think moving him to 3B would be best for the team.