He is reconciled to 「being outside of [not belonging to] the mainstream faction at the company.
I wasn't able to find 甘じる or 甘ずる verb in dictionaries I looked at. Is it a typo of 甘んじる?
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Considering this is an example sentence in a modern J-E dictionary, yes, I believe this is a typo. At least in standard Japanese, it should be written as 甘んじている.
BCCWJ corpus returned only one result for 甘【あまん】じる ("屈辱に甘じているのだ" in a novel published in 2002), and there may be a few other instances where old writers used 甘【あまん】じる. But let's not care about that too much.