Not if you get a good rotation. Generally speaking, the sweet range is probably more in the range of 55-70... so getting a bit more isn't that bad.
Once out of the cup, my general plan is to have set starters and backups... then in the scrimmage, get whoever didn't get to 48 minutes to that number. That will not only set them up for training, it will generally not harm their game shape (and may even increase it).
I currently have a 13 man roster... and plan on selling off a player after my cup run ends to get it down to 12. All but one player is at proficient or strong game shape.
[However, I am very strong for my current league, so it is a little bit easier for me to parse out minutes. On the other hand, I am still in the cup (and keep going on the road...) which makes it a bit harder.]