I know I might be on the other side of everyone, but if he isn't very profitable at this time, your numbers are likely way off. 10% penalty, but for him to get to 40% means that his AGI is at $151k already.
While I agree with others that a SB loan could be as cheap or cheaper than the penalty, there is some solace, even with the penalty, knowing that while you robbed some of your retirement income, you are free and clear of the partner and another loan payment. Your cash flow is also improved and maybe it allows you to contribute more to retirement sooner. I would recommend figuring out what you AGI was in 2015 and figure out how much it is increasing (based on more profits this year) and how much you need to take out. The $$$ you take out will be taxed at the rate above you AGI estimate for 2016. If you aren't very profitable year tax wise, your hit might be more in the 25-30% range with penalty, which may be worth it to remove the partner and a new loan.
Table 1. 2016 Taxable Income Brackets and Rates (Estimate)
Rate
Single Filers
Married Joint Filers
Head of Household Filers
10%
$0 to $9,275
$0 to $18,550
$0 to $13,250
15%
$9,275 to $37,650
$18,550 to $75,300
$13,250 to $50,400
25%
$37,650 to $91,150
$75,300 to $151,900
$50,400 to $130,150
28%
$91,150 to $190,150
$151,900 to $231,450
$130,150 to $210,800
33%
$190,150 to $413,350
$231,450 to $413,350
$210,800 to $413,350
35%
$413,350 to $415,050
$413,350 to $466,950
$413,350 to $441,000
39.6%
$415,050+
$466,950+
$441,000+