Here's what happened in SeaMonkey 2.48 on Ubuntu 14.04 :
1. I upgraded to NoScript 5.1.2, and re-enabled it (it had been disabled).
2. I decided to disable NS, and clicked "Disable" in the Add-ons Manager, but to my surprise I didn't get the dialog box asking me to keep the anti-clickjacking and other protections going and just disable script-blocking.
3. I restarted SeaMonkey. Button still appeared in the Status Bar.
4. In Add-ons Manager, I clicked "Disable" again, and this time I did see the dialog asking me whether I wanted to retain anti-clickjacking protection, etc. and just disable script-blocking.
5. I agreed to just disabling script-blocking.
6. I restarted SeaMonkey
7. The icon/button in the status bar disappeared. Additionally, the icon in the Add-ons Manager disappeared, like so:
(click on thumbnail for larger view)
At this point, I could not adjust any preferences for NS in the Add-ons Manager (clicking the Preferences button was useless), but I was able to disable NS completely.
EDIT: Shortly after I wrote this, I got notification that 5.1.3 has been released. I'll re-post after I test.