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.