The Crimea region was the only part of Ukraine that had a noticeable opposition (42% voted against independence). Even in the Eastern parts of Ukraine there was no region with more than 13% of votes against independence.
Donbas/Luhansk also ran referendums in 2014, along with Crimea, with ~90% support for independence. These polls were denounced as unconstitutional and illegal by Kiev.
And, while it was denounced as not a free and fair vote, realistically Kiev would not ever have allowed these votes to happen in any shape or form.
The second option was to be part of Ukraine. It was supported by 2-3% of voters with 80% turnout. I dont see a meaningful distinction between this and the previous status quo.
Even Kiev doesnt believe a vote without the troops would have had a markedly different result, which is why it rejects the idea of holding a vote at all on constitutional grounds.
Many in the USSR rejected the idea of Ukrainian independence based upon a similar principle of the inviolability of Soviet borders.
I think if the second option was status quo and Russian military weren't occupying the area, and the "stay with Ukraine" side had been allowed to campaign, I think the vote share for stay would have been much higher. Even ignoring the potential of voter fraud due to Russia not allowing real third party observers.
I don't know exactly what it would be or if it would be over 50%, but we should reject the obvious sham that Russia carried out.
Neutral sounds better than civil war.