As long as the higher salaries are based on a business necessity and are done in a non-discriminatory manner and/or have an impact on protected groups this would not be a problem under EO11246. Remember that OFCCP is not the "pay police" but tasked to evaluate compensation to ensure that it is administered in a non-discriminatory manner. As for the compensation directive, if you have a very small workforce it may not be possible to put together groups of employees that are similarly situated and have enough in a group to conduct a meaningful regression analysis. There are other statistical tests like Rank Sum, Fishers Exact, etc. that can be used for small groups.