The situation is complicated because John Deere leases out a lot of their equipment in a financial lease (they do operating leases too but they're not affected by this). In this sort of lease the ownership is technically with the lessee. So I can see the reason John Deere wants to stop people who legally own their tractor from tampering with software. It's still a lease and at the end of it John Deere might get back a working tractor (depending on the life of the lease), so they don't want it to have been used in any way that could damage it. It's a legal protection and I don't think it's as malicious as every journalist and commenter tries to say it is. If you look into their financials you'll see they have 10s of billions of dollars in machinery out that is leased out, they're just trying to protect it.
i mean, i don't doubt that the concern you mention might be part of it. but it sure is also a convenient way to lock people out of servicing their own stuff. and i doubt they're eager to give people the ability to service their own equipment without a strong public demand for that ability.
so the public should keep demanding that (as opposed to relying on the altruism of a large corporation).