Except that ignoring orders within one's designated command is one thing;
Except that ignoring orders within one's designated command is one thing; ignoring them in another general officer's command is something quite different.
And Fremont, although many things and not a West Pointer, had been a regular from 1838-48 (granted, in the CTE, with all that implies about independent command in the Old Army, but still); he had resigned in 1848 over a command issue, and so presumably had learned from that; and everyone of significance in the US leadership understood and accepted Magoffin's neutrality proclamation, because of what was at stake.
Say what you will about Fremont, but he understood politics.
Actually, the fact that Fremont did not intervene in Kentucky in 1861 is actually the strongest counter to your POD; if he recognized the issue in reality, why change?
And Fremont had a fair amount on his plate in Missouri, as it was, after all.
And the alternatives are even less likely; although Lyons, if he had survived Wilson's Creek, is probably more likely to WANT to seize the bull by the horns in regards to Kentucky, he was a soldier through-and-through. I don't seem him violating Kentuck's neutrality, any more than Anderson would have.
No, that took the military genius of Leonidas Polk.
Best,