If you’re wanting to replace all image markup with something custom, the best option is #2 – that way your new plugin controls everything relating to the gallery, and any future template overrides in WooCommerce will not affect it directly.
If it’s just the default lightbox you want to remove you don’t actually need to change markup or remove CSS classes; you can simply de-activate the feature. Thats explained here: https://github.com/woocommerce/woocommerce/wiki/Enabling-product-gallery-features-(zoom,-swipe,-lightbox)