The package says do not use with microwaves less than 1100 watts because it won't cook thoroughly. If I cook on a 700 watt microwave for 6 recommended minutes*(1+(1100-700)/700=8 minutes 10 seconds do I risk food poisoning or do I risk it tasting cold in the middle? I don't really know how these pies are made but the brand is banquet.
It doesn't matter for food safety how you reach the required temperature, as long as the food doesn't spend too long in the danger zone. Since you've looking at possibly minutes longer this is not a problem for you. Just make sure you know that the internal temperature is high enough when you finish cooking. I would recommend a thermometer.
Microwaves are notorious for cold spots. What is likely the issue is that a low watt microwave will not heat the food to safe temperature without affecting taste. i.e.Uniform cooking. For the entire food product > 165, some parts may have hit far far > 165. i.e. burnt.