In office 365, you can change the SharePoint Site Logo using CSOM Code. In this way, you can customize the host web using Provider hosted model. Below are the sample code to change the SharePoint Site Logo using CSOM code.

// Get the Web Object from the Client Context.

Web web = clientContext.Web;
clientContext.Load(web);
clientContext.ExecuteQuery();

//Update the SiteLogoURL property

web.SiteLogoUrl = web.ServerRelativeUrl + “/SiteAssets/myCustomLogo.png”;
web.Update();

//Execute the query.
web.Context.ExecuteQuery();

 Please make sure that your customlogo must have been uploaded to Asset Library before executing the above Client Side object Model code.

Happy SharePointing Folks!!!