As others have already said: allocating space prior to downloads doesn't use your internet connection, just the hard drive. One of the reasons to do it is also minimizing the risk of running out of disk space while downloading games.

There's a number of factors which influence how long it takes to allocate the files, e.g. the number of files the game has, but it definitely shouldn't take a very long time --- on my laptop's HDD it takes a little over a minute to allocate files for Civilization 4 Complete. If it happens again, then please submit a bug report via mantis.gog.com. In the meantime you can try temporarily disabling your antivirus when starting an install. Sometimes AV software decides it really needs to take a close look at some files :) We've recently fixed some issues with aborting installs taking a long time. The fixes are currently available on the public beta version (1.2.42), which you can switch to in Galaxy settings. If you're already on that version, then that sounds like a bug :) It might look like it started from scratch but it actually doesn't (unless the game's folder was deleted). It checks if the file has already been allocated or downloaded and if so, it doesn't try to allocate it again.