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Joining the Institute doesn't require you to kill or be enemies with anyone, however it is a Pre-requisite to the Underground Undercover quest which is the next main story quest for the Railroad after Tradecraft.
As for the ending, it is theoretically possible that siding with the Brotherhood under certain conditions allows you to remain friendly with the Railroad (although not vice versa). If that fails, just side with the Minutemen and make sure you are not hostile with either faction.