The things you're missing:

1. This requires root.

2. eBPF also requires root usually. As I understand it it was originally meant to be secure enough to allow unprivileged use but Spectre ruined that and now they've given up on that.

How would Spectre, a timing attack that does not require root, affect whether eBPF is safe to run as root?

It doesn't. Spectre means unprivileged use of eBPF is insecure.