Disabling the popup by crippling the executable is discouraged when there's a package manager. You don't know what else will break and updates may eventually reintroduce the file when you least expect it.
Instead you should find the package providing
captive-login and examine what other files it provides, usually with Debian derived systems you'll find that large software suites are split into several smaller packages.
You can find which package
captive-login belongs to with
dpkg -S $(which captive-login)
You should then list the other files it contains with
dpkg -L capnet-assist
In this case you'll see the
capnet-assist does pretty much nothing else than providing the
captive-login executable and some documentation for it. Knowing this you can then safely choose to remove the package
capnet-assist, for example with
sudo apt-get remove capnet-assist
Now the package manager is aware of the change and will warn you if any other package depends on
capnet-assist, in addition to not restoring the file next time
capnet-assist is upgraded.