The main problem is that saying Loghain should've removed Howe so soon carries with it far more negative consequences then it does positive. Aside from the military and economic considerations already brought up in that he controls the northern coast of Ferelden -- specifically the Pilgrim's Path, a vital trade route between Denerim and Amaranthine -- there's also how at this point there's no evidence of him doing any wrongdoing.
Oh, make no mistake, he has done wrong. And everyone knows it. But no one has any proof of it. There are only rumors and gossip about his part in the Cousland Massacre (although I personally found Howe's attack to be one of the most boneheaded moves he could've done) and although his rise to a position of such import is considered questionable, barring a Human Noble's testimony there's nothing to support it. And even then, a HN is considered to have suspect word because Howe has been spreading word around that the Couslands were traitors to Ferelden (which Howe honestly seems to believe, given that Bryce went to Orlais and Fergus is married to an "Antivan ******" as he put it).
Howe has made it a point to cover his tracks as best as he can so that no one can sufficiently challenge his version of events. Without a strong case to be made against him and support the decision, removing him does what Monica21 just said: it compounds and adds to his power-hungry image and ends up alienating more people from his aid (those loyal to Howe, those rebelling in the Bannorn, those who wish for more reason to take advantage of the vacuum, etc.)
So what would it look like if Loghain was to just remove one of his most important allies, slimeball that the man is, with nothing to really explain why? A bad thing, that's what.
Without Howe having enough rope to hang himself with, any discussion centered on how Howe should've been removed centers on hindsight. Should Howe have been removed? Yes. But let's not kid ourselves in thinking it'd be an easy to do thing that could be pulled off without a hitch.