(Relatively) recent Stanford graduate here, and former Frosh dorm RA. Not only is what you’re proposing fine, but I’d also strongly recommend taking that lighter load. A few thoughts:
In terms of the nitty-gritty unit count logistics, you’d be fine. WAYS courses can be as little as 3 units, so you can easily fit that into one of the other 11 quarters that you’ll be on the Farm. If you’ve passed out of the language requirement and/or calculus, then you’ll have even more free elective room. Even you haven’t, if you’re looking at the ChemE suggested plan #1A for example, you could make up the WAYS by adding 3 units into Junior Fall Quarter for a 17-unit quarter.
CHEM 31x is one of the hardest courses most Frosh will take, so you’ll definitely be glad that you have only two other classes at 14 units. Studying for these exams is quite time consuming…although they did change up one of the two professors teaching it this year, so it’s possible you’ll have an easier time with it than I did.
Something that all I and all RAs always told their Frosh—you’re bound to hear this several times from your own dorm staff soon enough—was that you should only take 12-15 units your first quarter. The lighter the better. There are many reasons for this, and you’ll be told that adjusting to living independently/learning your way around campus/settling into a college schedule/figuring out how to study in college “is a 5-unit class in and of itself.”
The most important reasons in my mind is that this is the quarter when you’ll be meeting the other ~70-150 Frosh in your dorm, and you should expect to meet some of your best undergrad friends within that group. Three of my own best friends from Stanford with whom I still keep in touch were in my Frosh dorm, and you’ll hear a similar story from practically every Stanford upperclassman and alum. As an RA, I saw many Frosh regret that they overcommitted during Fall Quarter—whether that be overcommitment in the form of classes, clubs, relationships, research, volunteering, and/or other assorted extracurriculars—and feel like they missed out on forming these friendships with their dormmates, having to play catch-up in the latter two quarters to fully integrate into the dorm’s social scene. Trust me when I say that you do not want to feel like you have to miss out on a social event with your new dormmates and potential friends because you had to study for a midterm.
Because it’s Stanford and many of the students admitted are the type who are used to having the most rigorous schedule possible, not all Frosh will listen to us. But practically all of mine who didn’t told me later that they wish they had…that was usually around exam week, when they discovered what 20 units’ worth of final exams and papers really meant.
tl;dr: Yes, skipping WAYS Fall Quarter is fine.
Good luck, enjoy your summer, and have an amazing time at Stanford! It was the best four years of my life, and you’re bound to make unforgettable memories and meet unforgettable people there. 