Conference is on the Yom Kippur holiday
Unless you're presenting joint work and had worked out your attendance with your coauthors in advance, not attending a conference is always your choice.

Not attending a conference for religious reasons is also completely standard and understandable. (Though your claim that Yom Kippur is just like Christmas is a bit unconvincing.  83% of Americans identify as Christian, whereas 1.4% identify as Jewish.  Moreover, a lot of Americans who identify as Jewish do not fast/atone on Yom Kippur and would be happy to attend a conference on that day: I do and I would.  Though not with as much glee as I would attend a conference on Easter, I admit.) I think it's an A-class excuse: i.e., if you tell this to your faculty advisor he will accept it without any comment.  I would keep to yourself however the fact that your amount of Jewishness is enough to get you out of a conference that you view as inferior but not a really important one.  That's not the most mature perspective, and if in your later life people observe that you seem to be using religion as an excuse to improve your schedule, they will not be so thrilled with you.  

By the way, I would think that there would be a lot of other reasons that a high school student could not fly to attend a conference.  Saying "Sorry, I've just learned that my schedule doesn't allow me to attend" ought to already be more than sufficient (B+? A-?). 

I think you may be off in your appraisal of the situation and the opportunity that going to any part of an academic conference is for any high school student.  My advice would be to, when you say that you can't go to this conference, tell your advisor that you really appreciate the mentorship and would be eager to go to a different conference, possibly a bit later on and/or during the summer.

Finally, your faculty advisor does indeed sound extremely nice.  Academics are extremely busy, and quality mentorship takes time and energy.  Your estimate that he spent half an hour looking at two drafts of your paper sounds rather naive to me unless he explicitly told you that.  I would spend more than 15 minutes looking at a student's cover letter, let alone their paper.  By the way, the fact that he is willing to spend the time probably means that he thinks you are extremely talented, so I hope you do not give up too easily.