Is it a good idea to omit part of a multiple surname for publications?
In Spain we typically have a very similar situation: two surnames, with the first being considered the most "important" in the sense that if we need to omit one, we omit the second. For example, someone called Juan García González can be called Juan García or Mr. García for short, but never "Juan G. González" as most US-centric systems would abbreviate it.

The typical approaches most researchers take are either signing just Juan García (omitting the second surname), or adding a hyphen (Juan García-González) to fool the American databases into thinking they are a single surname. Typically the first solution is chosen by authors whose first surname is rare, and the second one by those whose first surname is common and who would have ambiguity problems if they used the first approach (e.g. García is extremely common, so there can be dozens of authors called J. García, and therefore signing as García-González is probably a better idea).

Lately, a Spanish governmental science foundation has adopted these approaches as official recommendations, and many universities have followed suit and recommended them to their personnel as well. It's in Spanish, but just in case you are curious or it can help anyone else, here is the recommendation guide describing this: https://www.um.es/documents/793464/2907606/Recomend+Fecyt+DOC051115-1.pdf/0a403f57-253f-4f07-9bdc-762ff5a9a557

Thus, I think you should be safe both as Sobhan Omranian or as Sobhan Omranian-Khorasani, and you can choose between both depending on whether S. Omranian is common or not. I don't think adopting a middle name in your "pen name" would be problematic either, as you can always provide evidence of authorship of your publications if needed. But I would stick to the simpler, tried solutions just in case. If they are considered to work in Spain and even recommended officially, they should work there too.