No
Factually, they didn't. It has launched 14 more times with the NASA worm logo still on it, even during Starlink or commercial missions.
Why?
Elon Musk, and therefore SpaceX as a whole, are very conservative in weight. This makes sense, as for every 5 non-fuel pounds you add to the first stage of Falcon 9, you lose around a pound in payload. Obviously, this isn't great. Paint has weight. So here is a cost-benefit analysis:
Benefits: The worm logo suggests to some people that NASA owns it. This fixes that misconception.
Costs: Adds weight and therefore reduces payload. This is turn reduces profit from the booster and also means they have to slightly recalculate everything it does (since it has a bit more mass). That can get annoying. Takes time. Since workers time is money, this costs a bunch. Also, although I doubt they care that much about this, it the worm logo does remind people that this is booster was the first launch of the program that gave the USA access to the station by themselves for the first time in 9 years.
So, I think it is clear why SpaceX chose to keep the worm logo on, as the misconception can be very easily fixed (by simply explaining the story).