The way to solve it is to make the beaches nude-only. Then no anti-religious discrimination can be claimed: if they want to swim there, they just have to shed their clothes, and the rule is the same for everyone. Although, as a very fair-skinned person, the main problem I'd have with that is sunburn; I already like to wear a t-shirt at the beach for that reason.
If they get the prime section of beach, then everyone else is going to complain (rightfully) that the religious minority is getting special privileges.
If they get the crappy section of beach (relative to the nude and normal beaches), the religious minority is going to complain that they're being discriminated against.
You can't make a bunch of identical beaches. Beaches are not like software; you can't endlessly replicate them. Some are better than others, and they're a limited resource.
And finally, why should the country cater to religious extremists in the first place?
I know it for having found myself surprised to be on the fun part of the beach countless times.
That's a picture of a French minister crossing path with a local enjoying himself : http://www.directmatin.fr/france/2016-08-11/emmanuel-macron-...
Oh, and topless for women is ok everywhere.