If Mehmed Ali were somehow installed as Sultan (and I don't think this is possible through conquest - it would have to be through the death of Mahmud II), then the empire would probably look about the same, except it would be a lot harder to keep it together because Mehmed Ali didn't have the legitimacy of the Ottoman dynasty.
He would be out of his league versus the bureaucracy, and even if he did somehow manage to master it, he would probably quickly destroy the empire, since his motive was greed. His administration of Egypt and all his modernization programs were designed to extract as much money as possible out of Egypt with which to line his pockets.
If he were established as Sultan, that might change his attitude, since his desire for money and power were probably intended to raise his position in the context of the Ottoman world, and you can't get much higher than Sultan. Still, the Ottoman reforms of the 19th c were designed with the long-term in mind, and Mehmed Ali's were very short-term in conception. I think if you have TL with him in power you can pretty much send it any way you want.
It might send the Ottoman Empire down a more pro-French trajectory than it had in OTL (as opposed to pro-British).
I think it's pretty dubious that Mehmed Ali would have had any chance of seizing Istanbul after his victory at Konya. First of all, it's really well defended, not to mention across a body of water. Second, the powers, particularly Russia and Britain, would never allow it.
Most likely there would have been a standoff for a while while Mehmed Ali slowly bled to death financially, as Konya would have given him only an extent of the poorest portion of the empire with massive expenses to defend it. Syria, generally richer than Eastern Anatolia, was already a huge drain on Egyptian resources.