My clientand his girlfriend (opposite-sex) were domestic partners, so that she could get health insurance benefits through his employer. Then, they were married in October and filing married filing jointly

For the 1st part of the year, the health insurance benefits were reported as imputed income

What can be done with this imputed income reported on his w2? Will it go into his schedule A as medical or will he be able to exclude it all together?

It sounds like your client's employer provides health care benefits for unmarried domestic partners, but this is not a tax-free benefit (unlike health benefits for one's spouse). Consequently the amount of the benefit is included in his taxable income.

He has nothing to deduct here - you have said nothing about any medical expenses he incurred that he could deduct on schedule A. It's income, plain and simple.