I think you are overthinking this.. it disables ESX functionality with MSI-X, it doesn't actual disable the qlogic device MSI-X.
ESX driver is disabled, not the hardware.
IF VMware recommends it, and they posted a KB obviously it's a proven work around and they work with vendors such as Qlogic to TEST and verify it works properly.
They don't do it on a whim. It is safe, even if you aren't sure of the impact, if you want to fix the issue, I would follow their advice and not be concerned with fallout after the fact. You are doing it to resolve an issue which apparently you have, not doing it as a tweak.