I assume the top of your filter is below the level of the surface of your pond, if that is the case my first suggestion would be, raise the filter. If your filter is above the pond then I have misunderstood your post

If I have not misunderstood your post you can, as you suggest, draw only from the surface, ie over a wier, but that has the drawback you mention, ie it is sensitive to water loss.

An alternative would be to have a bottom drain in the pond with no lid and add a stand pipe to that, the top of the stand pipe being the wier. However, around the stand pipe place a bigger bore pipe with a castellated bottom, if the outer pipe rises above the water level in the pond then the annulus between the two pipes draws from the bottom of the pond, if you adjust the length of the outer pipe you could tune it so you get both surface and bottom draw.

A third option could be achieved by having the weir at the down stream end of your plumbing, ie discharge from a stand pipe etc above the filter, that would facilitate drawing the water from any level in the pond. BUT this idea is very sensitive to pipeloss and you would need to keep pipe loss to an absolute minimum. Pipeloss dictates how much the pond's surface has to be above the weir to push the flowrate through the plumbing, I may have this set up at some point in the future when and if I add a pond that is connected to my goldfish pond. The plumbing already largely exists for this and is 110mm sewer pipe for a 1600UK gph flow rate. My thinking is I will have the plumbing discharge into a shallow tank with a large perimeter, the flow over the perimeter/edge of the tank, wier, will be shallow because of the length of the perimeter and will therefore limit the volume of water that would draindown when the pump is switched off. The water going over the edge of the tank will be directed to a waterfall dropping into the lower pond.

However I still suggest raising the filter is your best solution.