Yes, it's fine. 

Your usage of *compromise* corresponds to definition 2 in the [Oxford Learner's Dictionary][1]: 

> ​[transitive, intransitive] to do something that is against your principles or does not reach standards that you have set 

> *compromise something* | I refuse to compromise my principles.

You can add a prepositional phrase headed by *for* to specify that you compromise one thing *for another thing*. **For** does a lot, as the [Merriam Learner's Dictionary][2] illustrates; two definitions that fits your use is: 

> 3b : used to indicate why something is done

> 5a : in order to help or cause (something)

The understanding of exchange comes from the interaction between verb phrase and prepositional phrase. You could compromise something (meaning you lose it), and you could compromise *for* something (meaning you gain, help, or cause it); compromising something *for* something defines both what is being compromised and what is gained/helped/caused. So my understanding would be that you don't want your group to go against existing differences in order to help advance a unique theory. 

In case that isn't enough, in a  [Corpus of Contemporary American English][3] search I found several examples of your usage: 

> Well, she's doing it for the dollar. And **when you compromise your values for money**, you know who you are. (ABC's *The View*, January 21st, 2016)

>  **We need to not compromise quality simply for the sake of structure**. (Karen DeYoung, "How the White House Runs Foreign Policy." *Washington Post*, August 5th, 2015.)

> Here, we remain vigilant about fraud and privacy, and rightly harangue Facebook **when its wizards compromise our secrecy for commercial ends**. (Julia Baird, "The Front Line is Online: Freedom Should Trump Privacy." *Newsweek*, June 14th, 2010.)


  [1]: https://www.oxfordlearnersdictionaries.com/us/definition/english/compromise_2
  [2]: http://www.learnersdictionary.com/definition/for
  [3]: https://www.english-corpora.org/coca/