Option 1:
4 efficient 6.5" component speakers (£180) and a small active sub like the little Alpine (£100). Fitting by a pro, possibly £200 plus, depending on where you go.
Active subs.
Option 2:
4 higher quality 6.5" component speakers (£270), a 5 channel amp (£250), 2 LOCs (£50), a slim subwoofer (£140) and cabling/dynamat/connectors (£80). Total £790 DIY.
Fitting could be £500+, but the job on the Civic is not hard, it just takes a bit of time. A keen amateur could do a nice neat job in a lazy day.
Car Audio Direct - The UK's leading car audio and stereo resource. Infinity Kappa 65.7cs - Infinity INF-KAPPA65.7CS
Car Audio Direct - The UK's leading car audio and stereo resource. Alpine MRV-F450 - Alpine ALP-MRVF450
Car Audio Direct - The UK's leading car audio and stereo resource. Stinger SALOC - Stinger STI-SALOC
Car Audio Direct - The UK's leading car audio and stereo resource. Blaupunkt THB250 - Blaupunkt BLA-THB250
Subjectively, using total guesswork and a few assumptions mixed with quite a few years of experience, mistakes and successes; if the OEM sound quality is 4/10, option 1 would be 6/10 and option 2 7.5/10. To get any better you need to dump the HU and replace with something nice (with proper time EQ) and build proper enclosures for the speakers.
This whole subject is so varied and there are so many opinions, this is just my take, so anyone else feel free to disagree and lob their own ideas in!
Warranty
If you make a claim on the warranty, the claim will be rejected if the fault is directly or indirectly caused by unauthorised work. So if your fancy speakers break the door card, then it's tough luck. But the rest of your warranty will be fine.