Still reading between the lines a bit and some of the above comments are a bit scary but true, unless you sort this out properly, but don't panic!
Firstly, if the 2K is for your shares, then it's subject to CGT at 30% but you have an annual exemption of €1270, so max tax here is 30% of €730, and you may have other losses to offset this.( As previous poster says, this should be on the market value of the shares, so I am assuming that if your wife accepts 2K , then that is the market value.)
The 9K loan is a bit more complicated. However, if's its less than 10% of the companys' net assets then there are no company law issues, just potential income tax issues as in previous posts. However, it may be that your accountant cleared this loan each year (through your payments re rent), and effectively gave you a new loan every year for 9K. If so, then you don't really have any historical tax issues on it-- just a current one and it sounds like the other partner is suggesting renewing the loan again, albeit in a back to front way!.
If your wife owes the company 9K then she must pay it back some day, else if this is never going to happen , then I reckon she is entitled to a tax free termination payment , which the company could award her and which would then allow her to repay the loan.