You could probably turn off the filter for part of the day without serious harm, but filters work best when they run constantly.
I think it's a better idea to modify the current from your filter so that the current is gentler. How to do this depends on the design of the filter. Some filters actually have an adjustment where you can reduce the water volume flowing through it. Read the operating instructions that came with your filter to see if this is true.
If your filter is air-driven, you can simply reduce the air flow. Get a gang valve (an air valve with at least two outlets) from the pet store and "bleed off" any extra air pressure.
Some filters allow you to change the direction of the output current. If this is the case with yours, have the outlet directed toward a wall of the tank. After the water bounces off the tank wall, the current will be milder in the rest of the tank.
You could also add a prefilter to the intake of your filter. You can buy these, or you can also make your own prefilter with some filter foam and attach it to the filter intake tube with rubber bands or zip-ties. Another version of this is to take a piece of mesh, such as netting or a piece of pantyhose material (washed), and put a few layers of it over the filter intake. The usual reason for prefilters is to keep fish fry from being sucked into the filter, but one will also obstruct the water flow enough to slow down the output of the filter.
Blocking off part (not all!) of the filter intake opening with a bit of plastic wrap of smilary material (held on with rubber bands) will accomplish more or less the same thing.
Any such obstructions should be added to the intake side, not the output, because back pressure on the output will make your filter wear out fast.