This is a pretty common challenge when organizing complex iAs. While card sorting is a great tool, it's not the only method available and sometimes might not even be the most suitable. Let's consider your options:
Reconsider the granularity:
You're right that cards in a card sort should ideally be of the same level of granularity. If your IA is too narrow, it may be worth considering if you can group some of your items together to create broader categories. You don't necessarily need to discard card sorting, but you might need to think creatively about how you define your 'cards.'
Use the tree testing method:
If your IA is deep but narrow, you might consider tree testing instead. This is a method where you test a hierarchical category structure, or tree, without the influence of navigation aids or visual design. Users complete tasks using the tree, and this can help you identify where they have difficulties navigating your structure.
Conduct a hybrid card sort:
If you have some higher-level categories that you feel are already well defined, you could conduct a hybrid card sort where participants sort lower-level items into these existing categories, but also have the option to create new categories.
Use a combination of methods:
Card sorting is typically used to establish a baseline structure, while other methods, like usability testing or content audits, can be used to refine and test that structure. If card sorting isn't giving you the depth of insight you need, you may need to use a combination of these methods.
Mix topics with different hierarchies carefully:
If you decide to mix topics with different hierarchies, be mindful of not confusing participants. You can provide clear instructions that you're interested in their thought process, even if it involves mixing levels of hierarchy. The results might be more difficult to interpret, but they could also provide unexpected insights.
User research is as much an art as it is a science. You have to balance the 'ideal' methods with what works for your specific situation. The most important thing is that you're involving users in the process and are willing to learn from them.