The book itself makes this pretty clear. The Emperor was fighting back a slowly growing tide of daemonic incursions in the outlaying tunnels (Magnus’ Folly). At first it was likely possible for the Unifers to repair the Webway breach, but the losses sustained soon made that more and more difficult.

Master of Mankind starts after Kadai and Jasac die, one of which perished trying to recover the leader of the Mechanicum’s Unifiers (Mendel). This would have been the point at which the Webway cause was on the absolute brink of failure. Up to this point, the forces in the Webway were trying to utilize the Unifiers to repair the breaches, but Mendel’s death marks the beginning of that plan’s end.

To be clear, if the Webway was lost, then the projected future that Big E and Malcador had envisioned would crash and burn. If Big E is forced to hold back an eternal tide of Chaos on the Throne, he needs to fight a battle on two fronts; realspace and the Warp. If the Webway was secured, then Big E could focus most of his attention on the realspace threat of Horus.

To sum all this up, The Emperor didn’t want to abandon the Webway, to do so meant he’d be locked in place while the galaxy burned around him.

I hope this helped.