This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate. 

How your team deals with DCMA pre-award survey results is the responsibility of the contracting officer with "senior level guidance" as your unit/command chooses to involve itself.  You will need to check with your agency/service to find out if it has guidance specific to your service/command. 

FAR part 9 provides information related to offeror responsibility, FAR 9.104-1, General Standards and FAR 9.104-3 Application of Standards. 

Should your team move forward with the award, it is important that you thoroughly document your rationale for making the award and all measures used to mitigate risks your team and/or DCMA identified.

It appears the primary concern is with the company's accounting system.  Assuming a firm fixed-price contract, our concern would be appropriately assessing progress payments.  We suggest creating unusual progress payments {FAR 32.114) to limit government exposure.