There were no crocodiles with crocodilian teeth when archeopteryx was extant? Seriously? Care to provide any evidence of that quite substantial claim?
Be that as it may though the fact that a bird like transitional has feature like a bird and not like a reptile does not make it less transitional if it still has distinctly reptilian features.
The fact that avians have a derived form of dentition distinct from the theropods just means that dentition is not one of the reptilian features archaeopteryx displays.
Any way in the same time of the archaeopteryx there was living a bird called confuciusornis it has no teeth at all and modern birds anatomy.
This is totally irrelevant unless you are using a twisted concept of transitionals, which seems to be looking like the case. No one is claiming that all moderns birds are descended from archaeopteryx so why should a contemporaneous bird with modern anatomy be considered detrimental to Archaeopteryx's position as a transitional?
TTFN,
WK