As this is a woodworking site with wood being our primary focus I think I should say that when you know the requirements of a desk (or any other project) ahead of time they should really be factored in from the start with the choice of material for the top. That's the right way to approach a build, rather than playing catch-up after the fact to get the thing to meet the usage requirements.
My question then is: are there any alternative desktop surfaces/coverings. Something: 1. that could be cut/made to fit 2. proper not-to-hard-nor-too-soft-ness for writing 3. functional mousing surface 4. of course the base protecting 5. And aesthetics
While you could in theory at least use a hard sheet plastic like acrylic or polycarbonate (including making a seamless joint if you're careful) the first thing I thought of that fulfilled all your requirements was solid-surface material, e.g. Corian. These are a composite material made from something like powdered marble and a resin binder and they are hard, opaque and durable.
But you'd probably want to think carefully about covering the desktop with anything that costs more than the rest of the desk put together O_O
Working more directly with what you have you might be able to do something with clear coatings.
The most obvious product in this area is a pour-on finish which goes on thick and sets hard and resilient. This wouldn't be an ideal solution for any number of reasons (possibly including cost again) but it might do exactly what you want and turn a softer-than-you'd like surface into a durable and long-lived one that can't be dented by writing.
You could try thickly varnishing it with polyurethane (multiple coats building up to a thick film, not one or two very thick coats). Even on soft softwoods this can be enough to reinforce the surface and make it strong enough, while not properly hard or resilient, to withstand the knocks and scrapes of daily use. You probably have some offcuts you can test this option out on and if it does enough I can't imagine it not being the cheapest of the possibilities presented here, but it would be slow to do and you'd want to wait at least a week after the last coat for the varnish to cure hard enough.
Edit: I should have thought of this myself but a friend of mine suggested something that would be effective here if, as with the solid-surface material, you don't mind that the wood is obscured and that is tempered hardboard. Cutting and installing it would be very quick to do and it's an inexpensive option at under $10 for an 8x10 sheet, possibly working out cheaper than varnishing and it's undoubtedly much more robust.