Its not up to us to tell you what you should or should not do here, but the facts are this :
As your wife, she will be entitled to state healthcare (but no pension) as your dependant on your Autonomo status.
If she buys and sells on e bay, and does not raise invoices / facturas and takes payments via somebody like worldpay or paypal, how are the Spanish authorities going to find out exactly ? I'm not saying that doing this is entirely legal, but there are far more people dodging the system in a far more blatant and visible way than somebody making a few quid online every month.
I'd just keep your head down.