Your reasoning may be right but I disagree with your conclusion. Remember that Angus King, former Governor and current Senator from Maine is an Independent. Perhaps Maine was the first state to use this system in order to make sure that third party candidates will always have a chance to win. If, as you say, Instant Runoff Voting helps the two major parties, why haven't all the other states adopted it as well? The reason is that once voters get used to the system, they'll realize that they finally do have the power to upend the 2 party oligarchy.
Last but not least, if you look at the official returns from Maine 2, you'll see that the first round is what is listed. The votes for the third party candidates are shown and the Republican is shown as having received the most votes. However, since a strong majority of those third party voters preferred the Democrat, he was declared the winner. Far from having their votes thrown away, those who cast votes for third parties, effectively had their vote count twice. Once for their candidate, and second against the Republican.