They're still very young. It will be fine in the end, pruning certainly doesn't kill tomatoes.
Pruning of most hybrid cherry tomatoes is good actually, 2-3 stems is the recommended rate. They usually have some multiflora gene, and pruning will encourage more flowers per truss, so total production will still be solid. Many OP cherries have the problem of having a set limit of flowers per truss of about 8-12, those are the ones people talk about when saying don't prune cherry tomatoes.
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