So I completed the BoS quest line and took care of the railroad and institute but "Taking Independence" is still available to complete, is this a glitch or can I still follow through the minute men's questline despite being the BoS's top dog?

The Minutemen are able to get along with just about everybody.

even though they want to destroy the brotherhood and institute according to the guide book or can you convince the Minutemen to leave the brotherhood be?

So they'd be fine with a BoS guy helping them rebuild the Commonwealth?

Heck, Preston thinks you should lead it.

The Minutemen don't engage the Brotherhood unless you make them hostile towards you. They were getting along fine with the BoS until I shot Elder Maxson in the face.

Hell, the Minutemen don't engage the Institute OR brotherhood unless you order them to.

Yep, I always thought of the Minutemen as building up my own power base