For convenience, I'd put a shut-off valve either side of the filter as you suggest. Depending on your layout, you might even want to put a drain cock there so you can empty the plumbing during the off-season.
Parts for that job are going to be under $30. Labor? I can't imagine it'll be very...
I've done something like this in the past, and I adopted your solution.
What I also did was carefully positioned the holes to be close to either the edge of the block, or near the reinforcing 'web' in the middle, so I could torque the bolts up good and tight and there would be some material...
My father built a greenhouse this way years ago - there was nothing special about it other that it was less sealed than a custom one. It was hard to make really waterproof without basically framing out a shed structure, and less sun got in because items like window frames and the structure...
I had some success with a heavily sanded ceiling (basically the same deal) by just covering the whole lot with 1/4 sheetrock as @Smiley noted above. It was an older house, so it also succeeded in leveling the surface.