A balance shaft delete is going to make it much more vibey, but it deletes about 8Kg of rotating mass from the engine so it also gives you a gain in horsepower and throttle response. I guess it probably depends on how much you care about vibes. CS documentation says "not recommended" for stock block, but I can't see deleting it doing any harm in and of itself. I guess a replacement balance shaft is going to have to come from an engine salvage. Mazda would probably tear your wallet a new one, if the quote they gave me on a long block is any indicator.
I think you need to add more oil to the engine after it's gone, too. Apparently aftermaket engine mounts are a requirement if deleting balance shaft, so I'd be suspecting quite a lot of vibration with it deleted.
You're braver than I am tackling this kind of engine maintenance yourself. I wish I was better at spinning a spanner myself. You seem more confident about it than most.
If your bores and bearings are OK - having bits rattle around and teeth missing from the balance shaft assembly is a bit scary - and you don't mind it being vibey and needing aftermarket engine mounts (I think rear mount is an essential anyway), and a replacement balance shaft isn't readily available, then I'd say it's a good solution.
Not sure re: which bearings are most likely to wear. I know cylinder 3 has a bad rep. Sounds to me like it's all worth checking.
"Blue Meanie" 2007 Aurora Blue MPS 3 - 18x8.5+44 SSR GTX01 - 235/40R18 Michelin PS5 - 3.5" ETS TMIC - CPE stg 2 mount - HKS/CPE BPV - 2XS inlet - 2XS short shift - Corksport turbo manifold - HT 98 octane tune - Leather/Aluminium handbrake - Momo shifty knob - 7" touchscreen - JDM Mazda Retractable dashtop screen assembly - Bespoke Raspberry Pi Android based GPS/Carplay and instrumentation - 36AH reserve battery and C-TEK isolator - TEIN Street Advanced coilovers 1" drop - Superpro bushings - 220Kw/410Nm.
"Lipstick" 2013 Velocity Red MPS 3 - 18x7.5+48 Enkei RPF1 -225/40R18 Federal RS-RR - CPE TMIC - COBB inlet - CPE stg 2 mount - COBB Stage 1 98 octane tune - COBB shifty knob - 2XS short shift - 2XS turbo manifold.