Reservations in this context could mean doubts, such as 'My mom had reservations about going out to shop."
This means that their mom was not sure if she wanted to go shopping or not because she has reasons not to.
what options do you have?
Muir's writing is on both the beauty and harshness of nature. He talks about the beauty of the flower he discovered, but then talks about having to go without supper or blankets and how storms and the harsh weather conditions became welcomed after probably showing up a lot.