To me, Earth 616 did not became a mess when Rachel Summers in the 80's and Bishop from the early 90's fled from their Earth's and lived on on Earth 616.
Likewise when the counterpart of 616 Swordsman was stranded on Earth 616 in the early 90's in the pages of 'vengers.
In the late 90's Nate Grey, Sugarman, Holocaust and Dark Beast also fled from their Earth to Earth 616.
All these characters did not, to me, make Earth 616 a mess to me.
I expect the new mainstream marvel earth post SW to also not be a mess.