It is totally fine to file the petition online and then to stay in Kenya. Biometrics for the petitioner are not standard, in fact the only times I've seen that is when there is a criminal history, or fraud is suspected.
Will your income be from a US sourced employer? You may also want to look into domicile as it pertains to Nairobi. Some consulates are strict about it, some are not. Maintaining things like voting record, driver's license, banking, etc in the US is a good idea.
I think the plan to live with your spouse while the petition is pending is a splendid one, particularly for an African consulate. Time spent together is the best evidence of a bonafide marriage.
Good luck!