This is the type of question that has no definitive answer, and you might get a bunch of different answers from different people. Really, it's hard to say definitively what Google thinks, and any answer is pure speculation and opinion.
That being said, my opinion is that this won't be overkill. Unless you're running an autoblog that makes 100 posts per day, I doubt that you'll reach the number of links that Google would use to classify you as spam. Sitewide blogroll links have been devalued recently, and in a similar way these sitewide links may carry less weight. Yet in and of themselves, they aren't going to get you a penalty.
The one thing you may want to look out for is the anchor text you use. If that anchor text is a keyword, you might get hammered for having low keyword diversity and being over-optimized (a la Google Penguin). I would suggest you either use a branded keyword (the site's name) or a naked url. In this way, these extra links kind of help you, as they balance out other links that you build with optimized anchor text.
I have a similar situation with two sites. They are related (which in theory helps) as they are both about education. I have yet to notice any kind of penalty on the main site because of all the links back from the secondary site.