protobuf: bump to 3.28.2, disable upb.

[wlynch]

I don't know why automation didn't handle this, but bumps protobuf to latest released version.

Also removes upb which is causing issues with downstream dependencies (otel-nginx - see https://github.com/wolfi-dev/os/pull/30305). I did a spot check locally and py3-protobuf and php-protobuf can still build.

Originally from: https://github.com/wolfi-dev/os/pull/30305 (couldn't include there since build was referencing older subpackage versions)

Related: https://github.com/chainguard-dev/image-requests/issues/4407

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