Alaska Ballot Measure 2 made two big changes to elections, both of which are expected to reduce the power of the main parties:
Party-run primary elections are replaced with non-partisan primary elections (sometimes called Jungle primaries). In a non-partisan primary, all candidates, regardless of party, run against each other in a primary election and the top vote-getters move on to the general election. Usually, in a non-partisan primary, the top-two candidates move on, but in Alaska's new system the top four move forward. This is because of the second change instituted by Ballot Measure 2:
The normal first-past-the-post system has been replaced with ranked choice voting among the top-4 candidates from the primary. Instead of casting a single vote for a candidate, voters rank their candidates. If no one receives a majority of the votes, the last place candidate is removed and their voters are assigned to the other candidates based on their second choices. This continues until one candidate has a majority.
The main advantage for Senator Murkowski is the elimination of the closed party primary. Murkowski's image as a moderate has made here popular with the state at large, but earned her enemies among the core of the Republican party. In a closed primary, she would have to win a majority of votes from the most committed Republican party members, where her moderate record would be a detriment.
This isn't just theoretical: in 2010 she lost the Republican primary to a candidate backed by Sarah Palin, before running anyway and winning election as a write in candidate. A non-partisan primary would let her qualify for the general election by appealing to all Alaskans, not just Republicans.
Ranked choice voting is (at least in theory) helpful to moderates. Even if a right-wing Republican made it through the primary, Murkowski, as the lesser of two evils, is likely to be the second choice of most Democrats and so she'd likely benefit from redistributed votes in the second or third round of the election.
Both of these changes mean that Murkowski has less need to toe the party line and can challenge Republican orthodoxy without worrying about being eliminated in a closed primary.
UPDATE as of March 17th, 2021: Indeed, the Alaska Republican Party has recently censured Senator Murkowski for voting to convict Trump at his second impeachment trial and is seeking to block her from running as a Republican:
The Alaska Republican Party has censured U.S. Sen. Lisa Murkowski for voting to convict former President Donald Trump at his impeachment trial and now doesn’t want her to identify as a GOP candidate in next year’s election, a member of the party’s State Central Committee said Tuesday.
“But it also directed the party officials to recruit an opponent in the election and to the extent legally permissible, prevent Lisa Murkowski from running as a Republican in any election,” he said.
Thanks to Ballot Measure 2, however, they have much less power to do so. While they could encourage another Republican to run against her, and might (I'm unsure about this) be able to force her to run as an Independent, they can't simply block her from the ballot as they did in 2010:
As for your second question, I don't know of any evidence that it was deliberately designed to protect Murkowski from a primary challenger. The "Yes on 2 for Better Elections" campaign pushes the idea of "accountability" and makes a big deal about Alaska's independent streak:
“This is a victory for all Alaskans regardless of their political leaning,” Shea Siegert, manager of the Yes on 2 for Better Elections campaign, said in a statement Wednesday. “We now have an electoral system that lives up to Alaska’s independent streak by saying ‘to hell with politics let’s do what is right for Alaska.’”
So I'd guess their intention was to weaken the parties in general, rather than to protect Senator Murkowski specifically.
I think that sentence is mainly a strangely worded way of saying that this is the expected effect of the change, not that the change was made deliberately to have that effect.