I myself use PayPal for STO and C-points, I've never had a problem like this, after buying points and confirming the transaction I am automatically re-directed to my STO account and logged out of PayPal. This would not be Cryptic trying to scam you, it would be PayPal f-ing up lol.
And yes I always check my PayPal after every use to ensure that I am logged off. To find that someone else is having this kind of problem with PayPal is worrying to say the least.
Purchasing Cryptic Points can only be done by logging into the STO website and passing through to paypal. So therfore STO should also log me back out of Paypal. If I were just making a quick purchase at work on a shared terminal then another user could come along after me and corrupt my Paypal account.
You have to log into Paypal separately. Cryptic doesn't own your rights to the account, if cryptic were able to log out - it'd open up the potential for them to log you in.
No, you need to practice better security and log yourself out of third party paysites.