Magnus is long past his arrogance and pride ,if he is given a chance to kill the man/god/corpse that is responsible for all the suffering in 40K im pretty sure that he will take it!
Even statues are good !

True, however if and I do understand that it is a big 'if', if the Emperor did reincarnate surely with the amount of power he has when in his current less-than-perfect state he would, in theory, be able to keep the Astronomicon going with a smaller portion of his power and still use his godliness to turn the tide of battle for the Imperium?
But yeah I get that this is all speculation, still..

it would make a great story if they pulled all the space marines back to defend against the chaos attacking from outside terra as well as the deamons coming from the warp inside it to give the emperor time to regenerate, david tennent would appear to save the day! =P

Yes, but then:
How many time would it take it for him to reincarnate?
Would the new child-emperor need to grow to maturity to be able to fully control his powers?
Would humanity survive without Warp travel in the meantime?
Wouldn't a new Eye of Terror destroy Terra if he leaves the throne even for some time?

Maybe the best bet would be for him to die and regenerate shortly after like all perpetuals, but if that would have been a viable option, why did the Emperor tell Dorne to place him on the golden throne in the first place?

because at that time no one else could, now however there may be people who can sit on it

I think Horus' weapon damaged him in a new way. or I remember seeing that somewhere.

If they Emperor came back, he might be branded an imposter. an anti-religion unsanctioned" psyker of immense power?

If he is indeed a Perpetual than there's nothing short of wacky artefacts like Fulgrite Spears that'll do it, and I don't think Horus had one of those with him at the time.
It's more the fact that Emps Plan B for the Throne - i.e Magnus - wasn't there so he had no choice but to sit there and hold the webway gates shut.

Magnus was plan A till Emps finished the human webway !But it never happened!

yeah, true, he was Plan A and Malcador was the 'oh shit nothing's working' plan B that wasn't actually a plan until it had to happen.

So I guess that the Emperor was plan C