I have a hard time understanding your adapted version of the sentence. If I look at the original sentence, and I replace all the medical jargon that I do not understand, the sentence basically says that in a certain process, something happens, and it gets a response. So basically, this sentence is similar in construction:
In the wedding ceremony, the minister's question is responded to by affirmative answers.
Now, your adaptation would be:
*The minister's question is responded to the wedding ceremony by affirmative answers.
Which, honestly, makes little sense to me. Not only is this used of responded to not grammatical, but it seems that you now make something respond to the ceremony, instead of the question.
Let's take apart the original sentence:
In the Golgi stress response, -> During this process
insufficient organelle capacity -> something (A) happens
is responded to -> something happens as a response to that
by augmentation of glycosylation enzyme expression and vesicular transport components. -> this (B) happens because (A) happened
So simply said: In this process, A is responded to by B. The to cannot be left out, because respond to is idiomatic. It means that B happens in response to A, or B happens because A happened.
Your adaptation would mean:
Insufficient organelle capacity -> something (A) happens
is responded to -> because of (B)
the Golgi stress -> this is the reason for (A)
by augmentation of glycosylation enzyme expression and vesicular transport components. -> this is how (A) happens. Or (B). I really don't know