Sorry about the length of this response. Outstanding loan principal is certainly part of plan assets.
I would amend the plan and the provisions regarding loans, to explicitly authorize the plan administrator to limit/adjust loans where necessary to otherwise comply with the code/regulations. Many plans have such provisions regarding deferrals - to meet non-discrimination testing without triggering distributions.
Similarly, the plan sponsor may want to curtail in-service distributions/withdrawals while a loan is outstanding.
Note that the rule for RMD's for a 401(k) is not the same as for an IRA - in an IRA, you calculate the RMD separately for each IRA, but you can aggregate the total and take the entire distribution from a single IRA. In the 401(k) space, you must calculate and satisfy your RMDs separately for each plan and withdraw that amount from that plan. So, there is no opportunity for the taxpayer to aggregate her 401(k) plans to satisfy RMD. The exception to that rule is in 403(b) tax-sheltered annuities, where you can calculate the RMDs for each plan and then take the total from any one (or more) of the tax-sheltered annuities.
Assuming the plan accepts IRA rollovers, and assuming the plan permits loan repayment acceleration (I would amend the plan accordingly if it did not so permit), the plan administrator would reach out to the participant and ask her to provide the appropriate amount (either in the form of an accelerated loan repayment or in the form of an IRA rollover), which the plan administrator will then turn right around and payout to meet RMD requirements. Assuming the individual just turned age 70 1/2 and the 1st RMD was due to be paid by April 1st 2017, I think you have a problem. The only saving issue here is that if it was the first RMD payable by April 1, 2017, we are talking about ~$1,679, where the $1,000 cash equivalent investment is just slightly short, and the 50% penalty would be ~$340.
However, if the next RMD is not due until December, I agree with the prior commentary that loan payments (no less frequently than quarterly, level amortization) should be adequate to meet RMD requirements for 2017. A $45,000 loan principal @ ~5%, repayments to be amortized over 20 quarters (5 years), means a quarterly repayment of $2,500+ ($10,000+ a year).
Assuming the plan document provides the plan administrator the authority to adjust existing loans, I would add a plan provision that all loans are subject to recharacterization into a distribution and a new, lower amount of outstanding loan principal to the extent necessary to comply with RMD requirements (or any other code/regulatory requirement). No cash is distributed, the recharacterization results in reporting a taxable payout (similar to a loan default at separation).
That said, I think it would be rare to see a situation where an individual had a vested account balance of say $100,000+, who took a loan of $50,000, then soon thereafter, ended up with an account balance of only $46,000, where only $1,000 is in cash equivalent investments and $45,000 is the outstanding loan amount. Perhaps you can get there if the plan allows withdrawals while a loan is outstanding, but, if it does, why wouldn't those withdrawals qualify to meet the requirements for RMD?