Impeachment isn’t the only way to remove the president. See previous discussions on Quo Warranto.
Additionally, if Obama were deemed ineligible to hold the office then the court could theoretically order him to vacate the office as he is illegally occupying it. There would be no need to impeach him as impeachment is a method to remove a legitimate president.
The Constitution declares that:
No Person except a natural born Citizen, or a Citizen of the United States, at the time of the Adoption of this Constitution, shall be eligible to the Office of President;
If someone is not eligible, how can they *be* President?
They can't. The Court's job is, in part, to enforce the Constitution. Congress can only impeach a President, which no one not "eligible to the Office of President, can logically ever be.
Unfortunately the Founders did not imagine someone not eligible being installed in the Office, so they provided no mechanism for removing such a usurper.