It's fine (although indeed a bit of a hassle), my only suggestion is to clearly specify it on the page of the game and/or when launching the game because it's not that common and not that long ago I launched a game which didn't and felt stupid after I started to mash all the buttons on my keyboard before coming to the conclusion that I had to plug a controller (I did and at least it was worth it as the game is great). ;)
I have yet to encounter a game that can be played with a controller, but not with mouse and keyboard.
A keyboard has like 10 times the buttons as a controller and if you give remapping ability, users will configure the game. You do not need to create the perfect control layout that fits everyone.
About the only feature a controller has, that a keyboard lacks is the analog triggers and sticks. And only if you need an accurate analog input, you will have trouble on a keyboard. Maybe throttle in vehicle games. And for something like a twin stick shooter, you have to utilize the mouse for directions.
Maybe look on /games/tag-twin-stick-shooter how those games deal with the keybord.
