This post is a bit long because I am citing SQF code and information from their guidance documentation. You are correct about the SQF requirement that the practitioner be a full time employee. It appears that your company is meeting that requirement. This is what the SQF code and guidance documents say about the SQF practitioner:
22.214.171.124 The senior management shall designate an SQF practitioner for each site with responsibility and authority to:
i. Oversee the development, implementation, review and maintenance of the SQF System, including food safety fundamentals;
ii. Take appropriate action to maintain the integrity of the SQF System; and
iii. Communicate to relevant personnel all information essential to ensure the effective implementation and maintenance of the SQF System.
126.96.36.199 The SQF practitioner shall:
i. Be employed by the supplier as a company employee on a full-time basis;
ii. Hold a position of responsibility in relation to the management of the supplier’s SQF System;
iii. Have completed a HACCP training course;
iv. Be competent to implement and maintain HACCP based food safety plans and food quality plans; and
v. Have an understanding of the SQF Code Level 3 and the requirements to implement and maintain SQF System relevant to the supplier scope of certification.
This element also includes the requirements for, and responsibilities of, the SQF practitioner. This is a key role within the supplier’s facility, being the person designated by senior management to manage the development, implementation, daily operation, validation and verification of the SQF System.
The SQF practitioner is the individual designated by senior management to develop, validate, verify and maintain the company’s Food Safety and Quality Plans, and assume control of the daily operation of the SQF System. The SQF practitioner may engage the services of an SQF consultant to assist with the development of the SQF System, or support its validation and verification, but overall responsibility remains with the supplier through the SQF practitioner.
The requirements of the SQF practitioner are clearly outlined in 188.8.131.52, and are further described in the SQFI guideline on SQF practitioners. Note that SQF practitioners are not required to complete an Implementing SQF Systems training course or Implementing SQF Systems examination, it is not compulsory although either or both is recommended. However the practitioner is required to understand and demonstrate knowledge of the SQF Code and its application within the site.
There is a designated SQF practitioner who manages the implementation and maintenance of the SQF System on a daily basis.
• The designated practitioner has the qualifications necessary to be an SQF practitioner (identified in 184.108.40.206 and 220.127.116.11) and is capable and competent to carry out this function.
• The designated practitioner has the support of senior management and has the time and availability to monitor the effectiveness of the SQF System; is competent and has the authority take appropriate corrective actions when necessary; and communicates to relevant employees any information necessary to maintain or improve the System.
Note the language used. It references a SQF consultant for the limited purposes of development of the SQF system and to support its verification and validation. It does not mention "contract" employees. IMO if you are contracted as a full-time employee then you should be good to go as the SQF practitioner. The site you reference may be using the phrase "contract position" in the sense of a contract service provider as opposed to an employee whose relationship with the employer is regulated through a term contract. A contract service provider will be issued a 1099 Misc and have no rights as an employee. Presumably you have withholding and take direction as an employee which invalidates you as a "contractor". Check with a SQF consultant to get a better understanding of this matter.
The question of what happens when the employee on maternity leave returns is another matter and would concern me as it does you.