So let's look at some scenarios where the Professor is able to defeat Victor Von Doom.
Scenario A: They both meet for the first time. Morals off for both.
Scenario B: Xavier has 24 hours prep time. Doom has none. Morals on.
Scenario C: Xavier has Cerebro and detects Doom entering the mansion. No prep for either.
Scenario D: Xavier as Juggernaut from the What If series. Doom knows about Cyttorak and its powers.
Scenario E: Doom raids the mansion and is confronted by Xavier, Jean Grey (no PF) and Emma Frost
Scenario F: Xavier has 1 week prep. Doom has Magneto's helmet on.