PHP is a terrible language in terms of design, but deploys are ridiculously easy, and refreshing a page is near instantaneous. There are plenty of other things to complain about with PHP, but part of its popularity is the relatively pleasant experience with the main tools.
Clojure deploys are pretty ridiculously easy - and refreshing pages on a Clojure based web stack is also instantaneous.
Seriously, Leiningen is great tooling. On pretty much every axis except startup speed I prefer it to everything else I've needed to use for work in other languages (Python, Ruby, and Node.js).
The main criticism I'd make, and this is something the boot (http://boot-clj.com) guys have mentioned (http://c2.com/cgi/wiki?CodeGenerationIsaDesignSmell), is that we are getting pretty dependent on code generation with lein templates, and they are getting increasingly larger and more complex just to handle our base scenarios (dev/prod builds, REPL, live reload). Maybe this is unavoidable, or not really an issue... I don't know.
I started using Django, as a relative newbie to python, back in 0.96, and it was a real pain in the ass to deploy. It took me a couple of days, minimum, all the while knowing I could have things halfway done in PHP.
Luckily I was given a stellar recommendation, and I stuck with it.
Django deploys now? Incredibly easy on the hosts I use (DO / Heroku). I expect Clojure to be the same in a year or so.
FWIW, I'm just starting to learn clojure. And just barely starting--these problems aren't annoying me yet.
I'd say it was there years ago. On Heroku you can deploy any Clojure project that specifies a ":main" namespace. Deploying Clojure to a VPN is no different to any other language that runs behind an nginx proxy.