I feel that a good and interesting game or story, should have moments of conflict like this. No, it isn't particularly heroic, and yes, it is very questionable morally. Without these kind of conflicts for the characters to deal with, you can lose out on development of those characters.
That isn't to say that I can't draw similar conclusions or parallels as have been mentioned here. I just think that if you PC everything, and make the characters objectively always good and always heroic, it can make for a bland story. If that is the audience and the game that you want however, more power to you.
I wholeheartedly agree. As a DM, I think it's great to occasionally throw something grey at the players, and leave it to them to work out what's best - it's often where the best role-play and character development comes to the fore. Some players will relish the opportunity more than others, so you have to be mindful of what gaming aspects your players like, but a lot of different player styles lend themselves to a dealing with a bit of moral ambiguity, and deciding which means they will try and justify. So the DM's primary responsibility, is simply to try and focus on what kinds of player responses you might encounter, and what the potential outcomes / responses might be - having clear motives for your antagonists / NPCs should be your primary focus.
So for example the Oracle/Giants need the relics - pure and simple. "Civilisation" i.e. the various humans etc of the Northern Cities, want to stop the depredations of the Giants, and getting the relics is going to help achieve that - a few broken eggs is the price one has to pay. The Uthgardt want to protect the mounds and their sacred relics, but I believe the relics and mounds all pre-date the Uthgardt, so really the Uthgardt are just the current-state owners, and the history of the North, and the Uthgardt, is that possession is 9/10 of the law, so if someone were to come along and take the relics, it's not much different than a bunch of Uthgardt raiders ravaging a local town and claiming its livestock etc. After all, the Uthgardt roam around the place, they are semi-nomadic, they tend to only gather at their mounds each Autumn. If someone pillages their mound, maybe even while they are away, yeah they will get angry and might go to some lengths to get the items back, but that's what makes for a fun story.
So by all means, leverage your personal distaste for the "white folk" beating up on the "noble savage", to help your players understand that this is a grey moral ground they are treading, and it's up to them to decide what's best. Embrace that, and leave it up to your players to navigate the outcomes. Just be prepared for whatever directions come about.