I bought a chicken that you cook in the bag. I put it in the freezer, when I took it out to thaw, I read on bag "Do not freeze".
Will it be safe to eat?
As far as food safety is concerned you should be absolutely in the clear - frozen food lasts way longer than refrigerated.
But I see two points why the manufacturer might advise not to freeze the chicken:
Sometimes chicken is treated (aka infused) with water and spices which plumps up the meat. The excess water might increase the cell damage that is inevitable when freezing meat, leading to more water loss when thawing / cooking and ironically "drier" meat than untreated. This may or may not be the case. The manufacturer might just want to avoid the inevitable quality loss any meat faces when frozen. Especially as the "ready to cook" packages contain a lot of air, which may lead to freezer burn over time.
If the chicken is intended to be cooked in the bag, this means the bag is food-safe and heat-proof, but not necessarily freezer-proof. Plastic foils for freezing need special chemical / physical properties or they might become brittle at very low temperatures, causing them to develop small cracks or tears, which can favour freezer-burn or, in a later step, lead to a leaking package when preparing the chicken. You didn't post the instructions for cooking or roasting the chicken, just be aware of the fact that the package may leak a bit and use a tray below in the oven.
Note that some manufacturers / sellers give freezing instructions for their chicken packs:
Morrison supermarkets PLC writes
Suitable for home freezing.
Freeze on day of purchase and use within 1 month.
Defrost in a refrigerator overnight.
Once thawed do not refreeze.
That won't be an issue as far as the safety of the chicken, if anything it might negatively affect the quality. It's never a safety concern to freeze anything that was safe before went into the freezer.