No, he shouldn't enter Miami. From a points perspective, he lost early last year, so not much to defend.
But, that's hardly a concern. Fed got back to #1 and got the record he wanted last year. I don't think points and rankings are on his radar any longer. For him, it truly is all about slams. None of these other tournaments matter.
He needs to rest, let the back get better and be fresh for the big push during clay and grass season. Also, Federer is looking to play for several more years. A knee jerk reaction to a QF loss in Indian Wells is pretty short-sighted, if he's only doing it for points.
Federer knows his body better than I do, so I think he'll do what is best for him. My guess is he skips Miami as planned.
He was clearly not 100% throughout the tournament and he lost a QF match to one of the 3 best players in the world. Geez. Not that big of a deal, IMO.