It is not litigation free. It is correct to say that employees cannot be treated as passengers for this purpose. However, still there is silver lining.
Hoever, in order to avail ITC, you will have to prove as under:-
(i) that transportation of employees from home to factory & back is an essential input and obligatory on the part of employer.
(ii) It is an input service for supplying output taxable service (supply) and used in furtherance of taxable business/supply.
The order of AAR Haryana in the case of YKK India Pvt. Ltd. reported as 2019 (22) G.S.T.L. 115 (A.A.R. - GST) = 2019 (2) TMI 1081 - AUTHORITY FOR ADVANCE RULING, HARYANAmust be gone through before arriving at any decision. In this case the applicant failed to establish that transportation of employeees was an obligatory on the part of employer. So his application was rejected.
Better to opt for filing an application with AAR. You can take cues from this decision for cementing your grounds of application before AAR.