Yes, although you might consider simply modifying the model architecture to remove some pooling layers if you find that 48x48 breaks some input size constraint. I don’t think 224x224 is a minimum for many models as e.g., 112x112 (and below) should work fine on ResNet-50.
The warning you see is for a slightly different issue. It is saying that you have to be careful about mixing upsampling/downsampling methods (especially across different libraries or library versions) as they can impact model behavior. It isn’t a warning that upsampling or downsampling is problematic in general.