Is it possible to delete REF Objects with CK/GECK?

Yes, but strongly advised against, as it would instantly make the mod which does so incompatible with any other mod that touches the same reference.

Crash to desktop level of incompatible.

Good practice is to disable the reference. Where a reference starts disabled and is later enabled by a quest, good practice would be to leave the quest scripts alone as far as possible, but either move the reference to someplace it'll never be encountered (like a Bethesda test cell) or to modify the dialogue/quest/story-manager conditions to prevent the reference being enabled.

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Deleting a reference in the CK might even result in a crash to desktop if there are no other mods, if the base game tries to do something with the reference.

My Idea is to make Concord to a Settlement. I would like to delete/ a possibility to scrap all Buildings arround except this one where you meet Preston the first Time. Its a very big and useless Town. And i think its a good Idea to make a really big Settlement out of it. So far i dont see any Relations to the Game or any NPC's so there shouldnt be any Problems (i hope). You are not even able to enter the Buildings. Its just useless Space.

The problem might still occur if somebody installs another mod which (for instance) opens up a bunch of sealed buildings across Boston so they can be entered.

Making the buildings scrappable would probably be the safer route to go down, or (as I said initially), disabling them.

If you do intend to delete any references rather than disabling them, it would at least be honest if you put a big warning on your mod's front page saying that it will crash the game at some point when used alongside any mod that touches the deleted references.

These are lessons learned by the community modding previous Bethesda games, and the reason that correctly cleaning a mod with xEdit (in this case, FO4Edit when it's properly released) results in any deleted REF's being undeleted and disabled.

Yea thx for the Infos, i will wait for the official Tools

No problem, and good luck with your mod - it sounds like a really neat idea .

Hopefully the tools will be out... fairly soon in the new year (fingers crossed). If you have Skyrim and have used the CK for that, then I'm guessing the FO4 CK will be very similar. Certainly reading up on the Skyrim modding guides will give you a bit of a head-start, without too much to re-learn.