I may be reading too much into this, but in this encounter I sense a definite Oedipal rivalry between Emerson and Muir playing out on Muir's part, at least. Muir keeps goading Emerson to spend the night outdoors with him under the trees. Emerson and his entourage demur; Emerson is old and frail. Muir could have kept company indoors with Emerson that evening--and who would have wanted to miss that opportunity!-- but instead went off by himself to spend the night alone outdoors, where he almost scathingly dismisses the famous nature lovers from back east. Here he is, under the trees and stars; there's Emerson, in a hotel room. So who's the man of nature now? Muir claims to be happier in his situation; but again, he's missing out conversing with Emerson for the evening.
It wouldn't surprise me if something unreported happened between these two, and Muir's pride was hurt. The Boston elite surrounding Emerson run into this seeming yahoo Muir, who enthusiastically wants to show them around...you can see how things might not work out.
But who knows? Fun to speculate though.
Source:
http://yosemitenews.info/forum/read.php?3,65448,65459