Please make sure you have followed these steps to install the module.
[Install the Azure AD Module][1]
Install-Module MSOnline
$Msolcred = Get-credential
Connect-MsolService -Credential $MsolCred
The throttling limit for B2C when deleting users is dependent on your environment. https://learn.microsoft.com/en-us/graph/throttling-limits#identity-and-access-service-limits
Based on the chart in the guide, your limit should be 8k request per 10 seconds, so about 48k requests per minute (which makes sense if you're hitting the limit at 50k users).
However, any request using your App registration, that isn't a GET has a limit, depending on the signInAudience (AzureADMyOrg, MultipleOrgs, etc.):
70k per 5 minutes
60 requests per minute (PersonalAccounts)
GET users has a base unit cost of 2, so you can technically only run 24k GET user requests per minute. But the Users endpoint for DELETE or POST appear to have a1 base cost, so 48k per minute for DELETE or POST operations.
From your initial post, it doesn't sound like you're using an App Registration, so the limit should be 48k requests per minute.
Limits can be increased via support request though too. You can create a free Subscription/Billing support ticket here.