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I think the important point is that DSpace's integration with the Handle System is *optional*. DSpace by default actually does NOT use the Handle System...all it does is provide tools to let you use it, if you choose to. Since individual institutions have to actually configure the Handle System for it to function, I always understood that license to "not apply" until you actually *choose* to use the Handle system. But, if you choose to utilize the Handle System, then you must register with CNRI to obtain a valid handle prefix (and also cannot build a competing system on top of the Handle System codebase).
As noted at the top of that license: "THIS LICENSE AGREEMENT APPLIES TO THE USE OF HANDLE SYSTEM TECHNOLOGY". By default, DSpace only redistributes the Handle System JARs (which is granted as part of section 2a in the license), and doesn't actually *use* it until configured to do so.
There's actually an FAQ related to that here: http://www.handle.net/faq.html#license
"I'm a new DSpace user. Do I have to pay for a prefix if I use the HANDLE.NET software? Yes. Anyone can be a Resolution Service Provider (RSP) and everyone must agree to the terms and pay the appropriate fees."
The important part is the "if I use the HANDLE.NET software". As a DSpace user, if you do NOT choose to use the HANDLE.NET software, you can still run DSpace and won't need to pay for a prefix.
If there are still concerns that you and others have, I can gladly talk more with the CNRI folks about the license to verify we are still following all the necessary license terms. But, as stated above, I think we are in compliance.