[Take into account that I identify as a cis-man. I actually would prefer some non-binary persons answering here, with their personal perspective, which I cannot provide. I just give this answer as a "patch" - until people with personal experience might give a better answer. I have made my answer a community-answer, so it can be improved collaboratively.]
How do non-binary people generally like to be referred to with pronouns?
There is a variety of proposed solutions. The following ones are listed in the non-binary wiki, take a closer look there for more details:
- die (in analogy to english they)
- er und weibliches Nomen (Er arbeitet als Programmiererin in seinem eigenen Unternehmen.)
- hen (inspired by the Swedish pronoun hen)
- sie und männliches Nomen (Sie arbeitet als Programmierer in ihrem eigenen Unternehmen.)
- they (using the anglicism they in German, even with the English declination)
- Vorname (use the first name)
Maybe with the exception of using the first name instead of a pronoun, none of these is actually established in the mainstream as of today. (I think I have read about x every now and then in some mainstream media before, mostly in language traditionalist articles critising it.)
Anyway, I think these might be the ways someone would like to be addressed. As far as I know, in English there is also some variety besides they, and arguments against using they. Still, I think it is fair to say, that they is far more common in English than any of the German possibilities listed above.
Does using the neuter pronoun es for non-binary people carry the same stigma as the English it?
Yes. It would carry an idea of dehumanizing or humiliating someone to refer to them with the pronoun es if they didn't explicitly choose it.
Can one use sie (plural)?
I think, people familiar with the English they would understand you. But don't expect people to understand you, it is by far not common.