Warning: Grammar terms vary.
Leaves is correct.
First let’s simplify for the sake of illustration:
Too many services enabled leaves an organization susceptible to compromised security . . .
Then add in the elliptical being:
Too many services being enabled leaves an organization susceptible to compromised security . . .
Note that we are leaving aside a relative clause reading — and therefore a plural (or even notionally singular) agreement — as it would be unnatural or would change the meaning: ?Too many services [that are enabled] leave an organization susceptible to compromised security . . .
The subject of your sentence (too many services being enabled) is a gerund clause with its own subject (too many services). The gerund clause’s subject does not affect conjugation. The gerund clause itself (like all gerunds) is singular in number.
It might help to see the clause in the active voice. For example:
Engineers enabling too many services leaves an organization susceptible to compromised security . . .
Back to the passive:
Too many services being enabled [by engineers] leaves an organization susceptible to compromised security . . .
It is the passive construction, with its two verbs (being enabled), that allows us to omit being:
Too many services enabled [by engineers] leaves an organization susceptible to compromised security . . .
You might want to write your way around any confusion, using an active voice gerund construction without its own subject:
Enabling too many services leaves an organization susceptible to compromised security . . .