Unless you're using Linode or something other general purpose VPS which you have installed a Minecraft server onto, having to use anything other than a WebUI to exchange files with the server really strikes me as sketchy. A dedicated can't-run-anything-else Minecraft hosting provider even giving random users SSH access is sketchy enough but requiring you to use it to update the game... that level of not having an IT guy is just a security nightmare waiting to happen.
Guessing by your comment that you've actually rented a general purpose Linux VPS and not gotten suckered into Honest Pete's Discount CreeperHost. In that case, carry on.
The last time I've rented a Minecraft server was probably over 10 years ago, and as far as I can tell, at the time having to upload stuff through ftp was normal.
Although reading this thread has also taught me that I know nothing about how deployment works and I need to catch up on that.