Although I hate defending corporations when they provide crappy customer service (which this is), I think what they charged you makes sense.
You bought 1 group ticket with 4 people on it, not 4 individual tickets, so the %15 fee would apply to the one ticket, thus why you were dinged for the whole value of the ticket. You could have bought the 4 individual tickets and mitigated that risk, but you would have paid more up front.
When re-issuing the ticket (i.e., they give you a new one for 3 instead of 4 people), they charge you what their rate is as of then, not what it was in the past. They purchase these passes from the EU rail systems, so they are charged what market is as of that moment. As well, since they had to send you a new ticket and process it, they would charge you the service fees (this should have been waived in my opinion, but it is in their right to charge you for it).
Since the ticket changes were initiated by you and not them, they have the right to apply whatever contract you got in with them when purchasing the tickets.
I suppose if you spoke with the right person you might be able to reduce some of the charges if they have the power (but I am just guessing as some companies have zero wiggle room when it comes to stuff like this). There is no law that says a company has to provide any sort of 'money back guarantee' when they are not in the wrong.
Now, whether or not the Eurail passes are worth it is another story...