Yes you should continue to do water changes.
If the water actually looks bad then I would start by doing numerous small water changes so you don't change the water parameters too quickly. (Sudden changes will stress out your fish). Do a 20% water change, wait a few hours, do another 20% change, wait a few hours and do another 20% change. Test your water for nitrate, nitrite and ammonia and if they are all where they should be, (nitrate: less then 20ppm, nitrite 0, ammonia 0), then you can go back to weekly partial water changes of 30%.
If you can siphon the gravel without danger to the fry then that would be a good idea too but watch out. Chances are that you've got considerable waste built up in the gravel and you don't want to stir it up as this may release anaerobic pockets of bacteria which can be deadly to your fish.
When you siphon push the siphon nozzle straight down into the gravel and don't move it until the water coming up is clear. Then take it straight out and push it down in another spot. Don't stir the gravel! If you've got rocks or other decorations sitting on the bottom don't move them just yet. Try to siphon under them without moving them.
Is there some other kind of filtration going on the tank besides the undergravel filter?
If there is considerable uneaten food floating around the tank then you are overfeeding.