The cost of the MS tool-chain is basically a rounding error on internal software projects. An enterprise MSDN subscription is a under 1% of my billable rate for the year and servers are ridiculously cheap even when paying for the windows stack. Now sure plenty of FOSS toolchain can work wonders, but when building small internal sites and compared to the Java stack we are simply far more effective.

PS: I have seen it both ways, Java redeveloped in .Net and .Net redeveloped in Java. Generally things where better in the .Net world. I spent years as a Java developer and find the idea of going back is horrifying.