She's been offered a permanent position but with a probationary period in between (3 months). She was 'head hunted' but clearly they are lowering the wage to allow for agency fees... If she was to refuse the job on grounds of salary could she then go direct to the company and talk to them?
I assume she's being paid a salary for the 3 months probationary period, not an hourly rate? If so, the agency will take a percentage of the annual salary. The agencies we work with vary in the percentage they charge.
The higher the salary, the more money the agency would get, so it would seem that it's the company the job is with that have set the salary.
When we offer a job role, we always go in at the minimum of the pay range to allow for negotiation if the candidate wants more. Your wife needs to be go back to the agency and ask for more money. I'd be surprised if the company won't move.