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A creature is hit by Thunderbolt Strike. If one of his allies is behind him when you knock him back 10' ...
I would expect the answer to handle Large Creatures either in the 5' space or being pushed through the 5' space as the feature affects Large or smaller sized creatures.
While it would undoubtedly be cool if this was a thing, it isn't.
Thunderstrike says (PHB p.62)
At 6th level, when you deal lightning damage to a Large or smaller creature, you can also push it up to 10 feet away from you.
So far , so hoopy.
Space says (PHB p.191)
A creature's space is the area in feet that it effectively controls in combat, not an expression of its physical dimensions. A typical Medium creature isn't 5 feet wide, for example, but it does control a space that wide. If a Medium hobgoblin stands in a 5-foot-wide doorway, other creatures can’t get through unless the hobgoblin lets them.
So, there is plenty of room in a creature's space for them to duck, jump or otherwise dodge out of the way of transient thunderstrike victims.
Now, in D&D 5e, things do what they say they do and no more; there is nothing that I can find that says a creature moving through another creature's space has any affect on that creature.
TL;DR
He moves through and past the other creature with no other effect.
