Agreed with Klein.
The moment we taken refuge with a Guru, we had made sure he is the one who bring us to enlightenment and one surrender oneself completely to the Guru, if we couldn't think this way, we should not take refuge under the Guru.
Yes, as human beings, we do have doubts. Every times we have doubts, we should recall all the good qualities a Guru posses, these including the great compassion, wisdom, the loves and cares, etc. He has all these good qualities since long time ago, remain unchanged from life to life.
Therefore, we generate full faith towards our Guru. He is not doing things for us for his own preferences, but for us personally, to customize an enlighten path for us. This is how compassion a Buddha is, yes, a Guru is our Buddha.
So by following any instructions from the Guru, no matter what action it is, it generate merits.
I do not think a Guru will ask the student to do something that against their refuge vows, as Guru is the one that gave us the vows.
I saw a debate before on Guru Devotion asking question about, "If a Guru asks u to jump over a bridge, will you do that?" For me, the answer is definitely yes. The next question from the debater was "But you will loss your life?"
I wasn't in the debate, but personally I compare my life and my Guru's instructions, certainly Guru's instructions are more important as this Guru who I have full faith with, knows my life better than me, so he definitely have better decision towards my life instead of my own decision which arise from selfish reasons.
There's a very fantastic book on Guru Devotion is the 50 Stanzas of Guru Devotion by Ashvagosha, also known as Aryasura and others names. I think it answers all my questions in Guru Devotion. There's a verse saying:
"It has been taught that for the Guru to whom you have pledged your word of honor (to visualize as one with your meditational deity), you should willingly sacrifice your wife, children and even your life, although these are not (easy) to give away. Is there need to mention your fleeting wealth? "