You can still name your son in his birth certificate as Christopher to honor your brother-in-law. But you can choose Topher as a nickname (as in the actor Topher Grace?).
I Uncovered a Family Secret After Choosing a “Forbidden” Name for My Son

Naming a child should be a joyful milestone, but sometimes, the choice can stir up emotions no one expected. This new mom kept her baby girl’s name a secret until the last minute, hoping to surprise her family. But when she finally revealed it, her decision sparked a reaction that could change her relationships and possibly her life forever.

Talk to your dad privately.
Try having an open talk with your dad. Let him know that you get why he’s feeling this way, but also share why the name Chris is so special to you and your husband. Explain that, for you, it’s all about creating new family memories. Sometimes, a simple, honest conversation can help clear the air and open the door to healing.
Use a nickname or middle name.
To ease some of the tension around the name “Chris,” you could try using a nickname just when your parents are around. Options like “CJ,” “Kit,” or even his middle name might work. This way, you’re keeping the name that means so much to you while giving your parents a little compromise to make things easier for everyone.
Write a letter.
If talking about this feels too hard, try writing a letter to your dad instead. In the letter, you can let him know you didn’t know about the past but now understand his feelings. You can also explain that you chose the name Chris out of love and to honor your husband’s late brother. This way, he can read it when he’s ready, take some time to think, and hopefully start to accept your choice without feeling rushed to respond.
Parenting has really changed over the years. Things that used to be seen as “bad parenting” are now just part of raising happy, confident kids. It’s amazing how these once “unacceptable” ideas are now the new normal.
Comments
I'd stick to your choice of name for your child. The reason you chose this name with your husband and father of the child is beautiful and honourable. If your husband and his parents are ready to have his dead brother's memory honoured in this way, surely your Dad is big enough to accept it.
Speak to your Dad, but have a letter ready to hand him if he won't listen right now.
But stand firm in your choice of name.
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