The question, as asked --
have there been any breaches of the prime directive by any space-faring civilization in the entirety of star trek lore?
-- is a bit difficult to quantify.
Not all space-faring civilizations have sworn to uphold the Prime Directive. It is alternatively correctly called Starfleet General Order 1.
To that end, it is arguable that species which even belong to the Federation have no compunction for maintaining the 'social development' of any culture they come across. It is primarily a Starfleet ethos and needn't apply to other races or civilizations.
With this in mind, remember that planets do need to apply for acceptance into the Federation. As evidenced in the episode Attached, civilizations such as the in-fighting Kesprytt can be denied for failing to uphold a certain standard. Riker presides over this decision; as a Starfleet officer his decision would be informed by his training. By abstraction, it would be difficult to gain admittance to the Federation if one were acting in opposition to the Prime Directive, especially if Starfleet were to review said admission.
Memory Alpha provides an excellent resource for the implied and explicit limitations the Prime Directive is intended to set.