Uh, you are totally missing the anti-Wallace movement by major democratic leaders. FDR was not convinced by his advisors. Wallace was defeated due to political maneuvering by major democrats at the convention.
It was a wartime party unity move by FDR to not make a forced stand of support for Wallace in 1944. Being President, FDR could certainly have shut down the Anti-Wallace movement, and he would have been broadly supported in doing so: 65% of voting Democrats according to the
Gallup poll taken at the time of the convention supported keeping Wallace on the ballot.