Assuming you've submitted the logo as a typical inbound=outbound contribution, you still own the copyright on the logo, but you may not forbid anyone else from from using the logo on copyright grounds, due to the permissive copyright grant you made via the MIT license. Effectively, the exclusive rights that copyright law granted to you to reproduce and modify the logo are no longer exclusive to you: you have offered those rights to the public at large.
The trickier aspect of this legal situation is not copyright, but trademark. Trademark allows exclusive use of a mark to identify the source of goods or services. A trademark might be a simple non-copyrightable phrase like, "I'm lovin' it," or may be a copyrightable work like a logo. Specific colors can also be trademarks. Normally, trademarks are formally registered, but at least some jurisdictions recognize the existence of de facto trademarks: if Entity X has been using Mark M exclusively in commerce to identify themselves and their goods, a court may forbid another Entity Y from using the that same Mark M to identify themselves.
Since this company has been using this logo for at least some time (this includes prior non-commercial use by the open source project), it is at least possible that a court will recognize the company's exclusive right to use that logo as an identifier. This doesn't forbid anyone from using the logo in a non-identifying context, like within an original work of art, but it may forbid use of the logo in any context that might convey false association with or endorsement by the company which uses the logo as its trademark. Neither your status as the mark's author under copyright, nor anyone else's status as recipients of copyright rights under the MIT license, gives any rights to usurp the current vendor's exclusive right to use the mark as an identifier under trademark law.
I want to be clear that, without more facts, I can't even begin to armchair-speculate how a court would rule with regard to a possible trademark case, but I simply wanted to highlight the potential application of a trademark monopoly in this case.