"Is the company removing this competitor from the market hurting competition in their own market in the long term?"
It's way better for the market to let the cash-rich large corporations attempt to develop their own competitor to a new threat they might see in the market than to allow them to buy that competitor.
It would've been better for us if Instagram was never bought by Facebook, Admob never bought by Google, and so on.
Sure, maybe they wouldn't have gotten quite as successful on their own, but for one perhaps Facebook wouldn't have become as strong as it became in the social media space (a good thing) or they would've been forced to create a NEW competitor, and we all benefit from more competitors in the market. Instead they removed one and made themselves even more powerful.