Just go in and be honest. Tell them what you've said here, but in a less post-ey manner. That work said they'd sort it out. That they scheduled you for things but said if jury duty came up you'd be free to do it. Something complicated the matter they planned for but it's by no means an unworkable situation and you're not even the top tier talent they rely on but they'd still like to have you not do the service because it'd make things easier for them.
If the judge says you still have to do jury duty then you have to do jury duty. Represent what they're saying fairly, but also represent your own take on the situation, as accurately as you can (without you saying they're shites and you want a jury duty holiday.)
If you do do dury juty, and the employer then gives you grief, go straight to the judge. There'll 100% be an avenue for you to communicate with him and her about personal and work situations that arise. The jury duty service is fairly well managed and they know it's out of the ordinary for people called, whether it's work or self-employed situations, childcare situations, education situations or medical situations. They do not want to screw you over and do want you to be able to complete your service as an honourable Irish citizen.
Remember, they deal with this stuff every day. And if you do end up getting excused, then you still did what was expected of you and it was never in your purview to decide.