Yes. Don't let Bob make a lightsaber, or don't let John denounce him (probably requiring him to make another character), or don't have the Master ban lightsabers.
From Bob's perspective, John is exhibiting 'My Guy' syndrome. Bob wants a lightsaber wielding Sith and John is saying he can't have one. Bob is thus justifiably upset because saying "my character wouldn't let the game be fun" isn't a good reason not to let the game be fun. You can look at other questions about 'My Guy' syndrome and how to deal with it on this site for more information.
From your question, though, it looks like there might be more at play here. John has chosen to play an extremely loyal character, and may feel like he is being forced to play out-of-character just so Bob can have a toy it doesn't make any sense for him to have. Bob getting his lightsaber and John not getting to do anything about it doesn't just get Bob a lightsaber, it changes John's character in fundamental ways without him having any say in the matter. John, then, is reasonably upset that he's being told "Sure, you can play this character, who you are actually interested in playing" and then told "We're just gonna ignore that now".
The difference between this and "My Guy" syndrome is that John actually want to have That Guy. He may well not be trying to play this character because he feels like doing a different character would be 'bad rp', but because he wants to play this character he came up with, who would act in certain ways, which hadn't previously been a deal-breaker, but now are being disallowed.
Coming up with an excuse as to why John doesn't have his character tell Master Splinter that Bob's character broke the rules doesn't fix anything here: at best the answer is "you haven't told him yet because (you don't know about the lightsaber, there's no call boxes on Venus, you think you did but Bob impersonated him, etc)" and John's character will find out and tell Master Splinter very rapidly, or be forced to carry the idiot ball.
Essentially what you need to do is figure out a few things, and then make a decision. The things you need to figure out are:
Can Master Splinter just not ban lightsaber making?
How important is it to Bob that he gets a lightsaber?
How important is it to John that he plays this character?
Is being in-character something your group values? (Hint: John's answer is yes, Bob's answer might well be no.)
Is stopping other party members from getting loot ok?
What makes Bob's character being ratted on a problem?
Would it be a problem if it happened in the first session instead of in backstory?
And then, assuming no solutions equitable to both people show up:
Who are you going to side with this time? (Siding with one of them is the right choice. Compromise solutions here will just make both players unhappy, unless they are fake compromises (like you were suggesting in your question) which will just make John even more unhappy than siding with Bob in the long run)
Why are you siding with them?
Are you consistently siding with the same person on these kinds of issues? If so, think about that and reconsider your choice.
Some groups I've seen find it useful to explicitly note that e.g. John is changing his character so the Bob can have a thing, so that abusive situations (where one person gets all the things at the expense of another) are easier to detect and diffuse. I haven't found this necessary ever, but you could try it.