Using Spotlight to play iTunes songs causes another song to play after resuming from pause
Unfortunately there’s no ‘fix’ for the described behavior that I’m aware of.

However, there are a lot of free/paid utilities that will not only do what you need, but also improve the experience overall. 

I could list you a dozen utilities but instead I will let you do your homework and decide what’s best for you. This list contains an important amount of utilities for iTunes controlling.

I can tell you which ones I use and my experience with them. 

1) Coversutra: It’s a very well designed paid application. You can check their website for a more comprehensive summary (and a trial). The developer (Sophia) reads the suggestions and bug reports. 

Pros: It’s very good for searching, very good. Think of a spotlight music dedicated. You can easily switch between playlists, songs, artists, etc. All from the menubar. (I activate it with shift + cmd + space. It also has a controller where you can define your keys for showing album art, define song rating, next, prev, pause, etc. The typical controller stuff. You will rarely need the keyboard. 

Cons: Although it has been optimized several times and results come extremely fast, scrolling the results is not as fast as one would expect. Sometimes certain actions might need a “click”.

All in all, it’s a product that works fantastically for me.

2) Launchbar: I use Launchbar for everything, and sometimes for music too. Since it has iTunes support, you can easily type the name of a song/artist/list and will happily play it. What it does is create a playlist called Launchbar and whenever you make a selection, it adds the relevant songs to that list, therefore when you pause/play, things work normally. You can also do the same things (pause, play, next) from launchbar. 

Pros: It’s also very fast and it does a lot of things (can’t live without it!)

Cons: Might be overkill for a song launcher/iTunes controller only.