This subject comes up at least once around this time every one of the 20 years I've been a member here. While the above is absolutely true, it's also true that many in your situation DO file as single, then later amend their return after their spouse arrives. I'm one of the many. If you are employed by the IRS you would not be asking this question. To my knowledge, the only people who would pay any consequence for filing with the "wrong" filing status are IRS employees. For the rest of us, filing as single when married means we will (at least theoretically) OVERPAY OUR TAXES, for which there is no "penalty".
So no, it is not a negative for your spouse's immigration to have filed as single. Consular Officers see this all the time and understand the reasons why. For example, I used my refund to finance my second visit to my (now former) spouse in China. Amended the return once spouse and step daughter had SSNs.