If you need to use many to many relationships or have relationships in general, then you have to have a model created using Power BI Desktop.
I am a little surprised that 1GB table is too big, as it should get compressed to about 10% of its uncompressed size which should be well under the 250MB limitation of Power BI.
There are certain things you can do to make the size of the model smaller so you may want to search the web on how to do that (too many options to list here).
The bad news is that until SQL 16 is out, Power Desktop is the only option for you to do Many to Many in memory, otherwise, I would recommend that you build an Analysis Services model and expose your data that way.
I would definitely investigate why 1gb makes to big a a model first though, there might be some low hanging fruit there.
@mageeb May be its worth trying below. (I have).
I had relational db with many PK FK relations and to not wanting to do this manually in powerbi desktop, I initally connected to my database using DirectQuery. Once connected and saved pbix file, I changed it to import by clicking on the link on bottom right which says 'DirectQuery enabled click to change'. This helped me replicate my db PK FK relations without needing to create manually.