I would suggest including basic brand guidelines as well as a rationale for even a simple logo, as a standard process for logo development and within your master logos supply. That way, even if the logo or brand has an abstract meaning, it can be explained and understood by viewers and HOPEFULLY the importance of brand consistency can enforced.
In saying this, I see your point that it is truly up to the individual business/company or even department to make sure that the brand is not eroded by someone who simply needs to use it but lacks an available EPS or even the knowledge to not change it. Maybe upload the brand guidelines to "Brands of the world" website for the public to have access to the brand guidelines if needed
Depending on how the logo development was "sold" to the client initially, it may be within the rights of the original agency to make comment and uphold the brand guidelines as a term of the 'license' from which is was sold. E.g. by the client misusing the brand, it may breach the 'license' of use therefore creating a negative reputation for the designer if the design is associated with the design agency (I assume that the copyright will not remain with you as a designer because you were employed by the agency and usually they get you to sign a contract that says that anything you design is the copyright of the agency. It all depends.)
So as annoying as it all is - I would say (although this doesn't help the emotional connection with design and design responsibility):
Push on and move on to greener pastures. Sometimes people won't see the same value in design and they will erode the brand. You can set the standards and try to educate your clients but really if at that point they still do not listen or care – you have to weigh up how much time and energy you will spend and maybe your design skill and education will be much better utilitised telling someone who is more open minded. There's plenty to do in the world for design and with one that won't listen, they'll be one that will.
Those who don't see the value of design will learn eventually by the success of those that do.