Such a vast empire is bound to get split at some point, particularly after succession. You can either force it by causing.. an unfortunate incident, as Kyle suggested, or sowing dissent with a powerful king-level or powerful duke vassal of HRE who dislike their current liege.
Of note is that you can beat larger armies than yours with some clever warfare tactics. You are a pagan, and if the enemy hasn't researched Military Organization at least two or three times (unlikely, if you are that early in the game), then they suffer severe attrition in your territories. Also important is that hauling such large armies can take time, and would give you a few precious months of consolidating your troops and destroying some of their armies while they call their Occitan legions. Hopefully your realm is much more compact than theirs, and have ample naval access for quick transport on sea rather than by land.
If you deliver significant damage to them, factions within their empire might grow powerful enough to cause a civil war. This can give you a significant advantage and might cause them to ask for white peace to deal with troublesome vassals. This will give you some ten years of breathing room for you to expand and grow until they are able to strike again.
As you always have a casus belli against them, yielding some lands to them now without a fight might be a good longer-term strategy to reconquer them later when they are embroiled in another conflict -- particularly if you don't hold any of the counties in the duchy.
I'd say that holy-warring is still the most effective way, especially if you have the full force of an empire behind you. If you attack at a time where your enemy is divided (succession crisis, during another war etc.) they may not be able to call allies, while you have the full force of an empire with you. You should be able to grab a few duchies at a time trough holly war, and may even get them without having a truce.
Great Holy Wars will allow you to take a whole kingdom at once, but they are much more difficult. Other Catholic are more likely to join the defender than during a regular holy war. Still, catholics kingdoms tends to be quite divided.
Then, you will need to convert them. The most efficient way is to give them to vassals, who will each have a court priest to proselyte inside the demesne. Unless you are going North Korea style, you'll have to give them away anyway.
Another method, much more difficult, is to try to capture an heir to a big chunk of land. Go pillage the castle where he is. if you grab them young, you should be able to convert them to the One True Faith™. Their future vassals will not be happy, but maybe you can try to help him once he is on the throne.
If you capture one more aged, force them into a marriage with a Norse. You can get your dynasty on a foreign throne, but it will not be easy and requires quite a bit of luck.
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From some searching about, this appears to be intentional. Holy Orders will willingly fight Infidels (people of different religious groups) and Heretics (people of heresies of your religion). They will not fight people with whom you have Religious differences (people within your religious group who are not Heretics of your religion). For the Jomsvikings, this means they will fight any and all Christians, Muslims, Jews and Zoroastrians and they will also fight followers of the Old Norse heresy. They will not fight other Pagans (Slavics, Romuva, Suomenusko, Tengri, etc.)