Why are excess amino acids toxic?
Firstly excess amino acids are deaminated to form keto acids and not urea.
Urea is formed utilising the ammonium released as a consequence of deamination via Ornithine-Arginine cycle

Secondly the released ammonium is toxic because of two reasons:

1)pH changes in the tissues (as mentioned in the question)

2)disturbs the balance of K+-Na+ gradient between the intra and extracellular fluids.


  ammonium ions compete with potassium ions for inward transport, over the cytoplasmic membrane, via potassium transport proteins like the Na+/K(+)-ATPase and the Na+K+2Cl(-)-cotransporter. 


This causes increased demand for maintenance energy, caused by the need to maintain ion gradients over the cytoplasmic membrane.That is why converting the ammonium to urea is neccessary.

why amino acids are deaminated:
to form glucose via gluconeogenesis or to form anaplerotic compounds

why acidic group of keto acids fail to neutralise the basicity of ammonia:
because they keep getting utilised for the energy expenditure that increases in the tissues as mentioned above.