I already have active subscriptions. Is it safe to change the Subscription Engine for the site?
Yes, it is safe.
The Subscriptions And Recurring Payments 2 extension allows switching between eWay, PayPal and Authorize.Net engines without any negative impact on the running subscriptions.
To switch from one of the engines to the other, you just need to change the Subscription Engine setting in the General Options, then configure correspondent Subscription Types for the new engine, and assign them to the desired product(s).
After that, the new subscriptions will be accepted through the new Engine, while the existent ones will still be processed with their old attributes.