Good writing is the point
Doflamingo is in a lot of pain right now. Even if he sews up his organs, all that's gonna do is stop the bleeding and stop them from failing to work the way they should. His body, his organs, they're still in an immense amount of pain, which is just gonna go up as he sews up his organs with no anesthetics. Anyone who's had stitches will tell you, constant movement immediately after getting them will **** up the sewing and undo them, which means as Doffy continues to exert himself, his body is probably gonna have to constantly and passively sew up himself over and over, meaning more pain along with the added pain he's gonna get from Luffy.
It's a big price for the sake of keeping himself alive. Amazing testament to Doffy's pain tolerance.