I lived in Alaska when Palin was first elected as Governor, actually. It seems to me that, even if Murkowski gives her the senate seat instead of his daughter, Murkowski is still going to go down to defeat in 2006. His governorship was not well remembered, and Lisa Murkowski's rise to the Senate didn't have much of an impact on it. In fact, despite the hot air of the time, Senator Murkowski went on to win an easy reelection (and, as we all know, a not-so-easy one as well)
We might very well see Sean Parnell running against Governor Murkowski in 2006. His father was a former Democratic candidate for the House (meaning both father and son were defeated by Don Young!) and he, himself, had served in the state legislature and senate as a Republican. At the time, he was a prominent lobbist. If the field looks open, he might decide to make a run for the governorship instead of Lt. Governor. If not Parnell, I could possibly see Ted Stevens' son making the run, he was the Majority Leader of the State Senator. Although I suspect the relations between the Murkowskis and Stevens remained strong.
I agree that Palin likely won't get the nomination for Vice President if she is in the Senate. She'd have had direct contact with McCain at that point, and I doubt he would have taken much of a liking to her after direct contact. Maye Libby Dole gets the VP spot? Certainly not Romney, as McCain and him never liked one another. I figure john McCain will want a lesser known figure with a vaguely reformist background to be his VP.