I've been building systems for years in numerous places. Have you never experienced a political situation where a decision is made in these systems you describe as beautiful and poetic, that is not your own and yet due to organisational structures you must obey? I am curious given your attachment how you handle these. They're standard political issues in organizations larger than a few people.
My attachment? That aside, I think what you're asking is really simple. Relationships and empires are built on compromise. When you work a job you should agree with the stated objectives of your bosses. If you've got those bases covered, and it's a healthy environment too, then nothing should surprise you.
