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This won't harm the battery at all. Most phones aren't sold with a completely dead battery, and it's actually better for it to be partly discharged if it's in storage. I would have been more concerned about the condition of the phone (where it's been bought secondhand) and leaving it for a couple of weeks without checking it over.
You may want to seriously look at opening the phone and examining it to make sure that there is no physical damage. If not, then wrap it back up and put it under the tree. You would be more able to file a "damaged in transit" claim with the seller if it is examined upon delivery instead of waiting two weeks. Then it would be your word against the seller that your new phone was under the tree and you didn't break it yourself.
Enjoy your new phone!!!
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