You may very well consider how they feel and what they might prefer but I would suggest a "harsher" approach.
If they have a job in Japan they should at least be familiar enough with the language to say:
Sorry, my Japanese isn't that good. Can we speak in english, please?
Honestly, even a written card with this on it would be fine.
Also you are likely not the only customer there so the clerk has to know somehow how to deal with people who only speak Japanese.
Further more you make the assumption that the person's English is better than their Japanese. This doesn't have to be the case.
For this reason I suggest starting of in Japanese and only switch if you see the person is really uncompfortable or straight up asks you to switch.