Does providing a noisy Vpp for a short period of time affect programming an EPROM?
What the datasheet is saying is essentially “don’t have Vpp on unless Vcc is also on”. It is perfectly valid to turn Vpp on and off while Vcc is on. In fact, normal operation would be to have Vcc on continuously while turning on Vpp only when you need to program the device.

You’re fine.