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How does GW feel about people using some of their other GW models as replacemant for those that have been discontinued? Like if for instance wanted to use a Biologus Putrifier in place of a Renegade Commander? For that matter what about other players?

As long as it's the same size and has the same weapons most people are going to be cool with it. It is likely up to each manager's discretion in terms of GW policy. I personally think WYSIWYG is very important for clarity and ease of play, but if you have that down I don't really care what model you're actually using.

Not sure about GW but I don’t really have a problem playing against anything as long as you’ve told me what it is beforehand. Your model seems to fit from a fluff point of view which is always nice but I’ve even had mates buy a new codex and proxy their old army as the new one until they built up their collection.

If you have a few stand ins in your army, it’s always a nice idea to make a print out for your opponent that tells them quickly and easy what each model represents in game terms.

General rules of thumb for "most" places you'll end up playing...

1) Should be around the same size as the model it's replacing.
2) Should still have appropriate weapons for the model it is representing.
3) Should not be on the table with another actual model of the same type which is something else (i.e. "this biologus guy is a captain....this biologus guy is a psyker...")
4) Put some effort in to meet the above criteria and don't be lazy.

You should be fine.