You have portrayed a very precarious scene of the situation.
We can approach the problem in a stepwise manner:
First, the point to be considered here is whether your partner & you indeed want to have the baby and if so, within or outside the wedlock for overcoming any hassles that the child can face in the future.
Second, if you both decide to get married then the next point comes about explaining the scenario to your partner’s son. Considering the love between you two, it is likely he will give his consent and provide you the due respect.
Many a times, we overthink situations and scenarios. It is best to face it.
The worst you have already thought over. Anything above this will be for the best.
Hope this helps. God Bless!