what should I replace resonator with?

resonator keeps Getting hit by road humps as car is too low.

Fixed that for you.

I want to stop this.

Easy.. raise the ride height.

I could heighten the suspension But I’d rather not.

Of course. sigh

I believe a straight pipe would be too loud.

I don't have any hard numbers but it's quite likely this would be the case - resonators aren't on there for sh#ts and giggles, even assuming a resonator delete didn't have negative effects on engine performance it would get very, very loud and drone-tastic. Your neighbours would hate you, your hearing would hate you, and a couple of motorway journeys later you would hate you. The sound deadening on 90's Civics is nothing to write home about - as was the case with many mass market cars of the era (excluding the luxury vehicles).

But not only would it sound awful you might even be able to collect a shiny Vehicle Defect Rectification Notice under Construction & Usage regulations and you'd have 14 days to put the resonator back, because c'mon who doesn't enjoy having to hurriedly refit an exhaust and then take the car to be checked at an MOT station?

Is it possible to buy a resonator which is maybe slightly bigger than the exhaust pipe diameter?

Maybe..tracking one down would be shopping advice and therefore off-topic here (I suspect owner's clubs and the like would be your best bet), but these aren't made to a size that's plucked out of thin air - the size and shape is designed so as to produce a specific effect and behavior on the sound waves produced by the exhaust and the engineering involved is decidedly non-trivial. Is there possibly a shape that would still "work" yet have a narrower diameter? It's not impossible I guess - but that sounds like a very niche item, stock resonators aren't that much wider than the actual pipe. However..

Whatever I put there I want the car to still sound decent.

Changing the shape of the resonator is going to change the sound of the exhaust, that's basically unavoidable - whether it's for "better" or for "worse" is going to be highly subjective and there's going to be no way of knowing what it's going to sound like without hearing one fitted.

So that leads you to the key choice - what matters to you more? The way the current exhaust system sounds or having the car sat on the floor? Given the innumerable other issues that come with running a car that's so significantly below it's stock ride height that it's hitting the exhaust on bumps around on UK roads brings I know what I would do but it's your car.