Worth investing in MS SQL? Not trying to start a war here, but I would like some thoughts.

I work for a small nonprofit that is eligible for generous charity licensing from Microsoft. I am the database/web coder and my background is with open source stacks. I am most comfortable using PHP and MySQL.

That said, we are undertaking some large projects and am wondering whether it'd be worth investing in MS Server 2012 as a data staging and reporting system. It would not be used for any production purposes. I am most interested in the server studio management's advanced capabilities for importing and exporting data and for little productivity boosts like Intellisense.

What do you think? Is it worth the 80% discounted costs, or should we remain open source?
Not worth it for the reasons you gave, especially considering that you're not going to use it for production purposes. Reporting Services is a great platform for reporting, but I'm sure there are Open Source tools and frameworks to help you with that for PHP / MySQL. Ditto Integration Services, especially in 2012 (much better IDE for developing packages) it's a great tool for ETL, data staging and other import / export work, but probably overkill for you.

I'd definitely stick with the open source for now - it's always going to be cheaper for licencing ;-). Especially as the cost model for SQL Server 2012 shifted to a different per core model. We had to disable cores on recent deployments to bring down licencing costs, as we'd bought hardware before-hand (on assumptions of the same cost model as before). Funnily, enough that's how I started out on SQL Server - with a "we must port this to SQL Server, because Oracle licencing just got too expensive" project.

I look after about 16TB of high-transaction throughput SQL Server production databases for international clients. So definitely not anti-SQL Server and make plenty of use of all those tools you mention.