IMHO, I think that it's not worth the trouble, risk of leak, or unsightly plugs that you will have to use. Depending on how much flow is generated by your return pump and the size of the overflow pipe, limiting the drainage system to one overflow may cause your system to gurgle.
A possible solution would be to increase the size of the remaining overflow plumbing, but that will probably require drilling tempered glass... we know how that ends.
At the very least, you should try to determine if the one overflow can handle the amount of water flow you plan to use. I'm no help in determining that. Maybe someone else will chime in here.