I would agree that it's not recommended for the reasons mentioned above. Nearly any glass shop will cut some glass for you and it shouldn't break the bank.
However, if you are going to try it, cut the acrylic baffles so you have a little room/gap between them and the glass sides. This will allow the expansion of the acrylic once it's saturated with water. Apply a bead of silicone along the lines of where the baffles where will be. Push the baffle in to the bead. Then apply additional silicone on the same side as you pushed the baffle in to re-fill the gap (for a lack of a better term). Smooth both sides as best you can. Just make sure to use plenty of silicone and let it dry for several days.
It may not look pretty and there is no guarantee it will hold, but I followed this procedure nearly three years ago and the baffles are still very secure. So it can work but in my opinion, and after saying all of this, I would still recommend getting glass cut and using it. It's what I did on the last sump I built.