Admittedly, there's still no good deploy solution for C# at the moment that isn't a colossal load of work, but web deploy is definitely not a good choice. It's like MS looked at every single choice and went "Hmm, we'll pick the worst of these two options!".
Good luck if you need to do a rollback stat.
VS + C# + Azure integration is excellent, and there is nothing which prohibits turning up a 2nd instance any more so than using AWS, Docker, Chef or whatever your choice may be.
I am also not convinced Visual Studio is a bad habit, as it has many features and tools which are often superior to open source alternatives (debugging, integration, intellisense). I currently use Vim + Golang and Emacs + Clojure; comparatively those environments do not make me biased enough to say VS does not have some incredible upsides.
My assumption is that most people may not have spent enough time with the Windows tools to judge them fairly as we have all been tremendously productive on Linux and there are ideological issues spawned out of the decades of Windows dominance which slant these discussions.
Is it alright for your site to go down for minutes?