Can you Repulse a Thwonk! that is repeated?

Yes — but only if both executions of the Thwonk! choose the same unit. Repulse reads "Counter an enemy spell or ability that chooses it and no other friendly unit," and Repeat doesn't create a second spell: it's one chain item whose choices are all locked in during finalization (Rule 820.2.a). So if the Repeat targets the same attacking unit a second time, the spell only ever chose that one friendly unit, and Repulse is legal — and because it's one spell, countering it negates both stuns (Rule 426.1.a).

If the Repeat instead picks a different attacking unit you control, Repulse is illegal — the spell is choosing two friendly units, so neither one is "the friendly unit and no other" (same logic as FAQ #12717 for repeated Existential Dread / Bellows Breath). Note the second stun on an already-stunned unit still counts as a choice even though it does nothing, since a stunned unit may be chosen again (Rule 424.1.a.1) — that's fine here, it keeps the spell at one friendly target.