Trust me, no one wanted the character to stay red more than me.
I'm acutely aware that when Flynn stole the other program's identity in the film, he remained red for a long time.
Without getting into a boring technical explanation: it's a limitation of the game, and simply not possible to make your player character red permanently. So the best that can be done, is to show an animation of the character briefly turning red, then back to blue. Basically, we'll have to look at it as you having absorbed the essence of the other program. And now that you have, other programs see you as red even though you're still blue.
There's an icon on the HUD that turns red, to let you know that you're currently disguised with another identity. It will change back to blue, or switch to another color, to let you know your current disguise or lack of one. Best I can do, I'm afraid.