Konami have already said they intend to keep making them, when it was first rumored he was out at the company they posted this statement. Also they supposedly posted a job listing looking to replace him, I don't have a link to that though and don't remember where I read that.

Here's the Konami quote:

“The latest entry in the series, Metal Gear Solid V: The Phantom Pain, will be released with Hideo Kojima as originally announced on September 1, 2015 in North America, Central and South America and Europe as well as on September 2 in Japan and elsewhere in Asia.

After the release of MGSV: TPP, Konami plans to also continue releasing titles in the Metal Gear series. We would like to offer our deep gratitude for your continued support of the Metal Gear series.”