For those in group practices, are your loan payments deducted from your "salary" in order to decrease your taxable income? Is this negotiable? Would there be any legal issues?

There's no reason to have your student loan payments deducted from your paycheck. The tax implications won't change.

Details: http://www.irs.gov/taxtopics/tc456.html

"You can claim the deduction if all of the following apply:
Your modified adjusted gross income is less than $70,000 ($145,000 if filing jointly)"

from the irs website
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Most docs, except for some primary care docs with non-working spouses, aren't going to qualify for this deduction. Not sure if there are any legal ramifications to having it deducted from your salary.

You could have the loan payments made by your practice on your behalf but I'm sure it would come out to you on your W2 as income. The loan is your personal obligation and not a loan to the corporation, LLC, partnership or whatever. If it is paid on your behalf, I think it would be a part of compensation. Even if it were a loan made to the practice, loan repayments are not deductible on the corporate books so you (and your partners) would have the paper profit show up on your K1's.
The IRS gets you either way.