Hello Alain,
at first glance I would say no, as the problem here is that the OP would like to use L3 MPLS VPN PE-CE links as primary links and not as secondary. He had p2p direct links so before he/she was able to prefer primary paths over VPN backups because routes were all of the same type EIGRP internal routes compared to EIGRP internal routes.
On the CE nodes eBGP routes are preferred over EIGRP internal routes by default for their lower AD (20 < 90), the problem arises if the VPN backup ( p2p GRE over IPSec or DMVPN I guess) is terminated on a different router.
If so internal routers in the site will compare EIGRP internal routes coming from VPN with EIGRP external routes that are the result of CE redistribution of PE-CE eBGP into EIGRP domain.
In a case like this the best solution may be the introduction of an additional EIGRP process on routers that terminates the VPN with appropriate redistribution to/from primary EIGRP process. In this way routes coming from VPN will be external routes as the routes coming from MPLS L3 VPN and are comparable. At this point just tuning the seed metric will make MPLS L3 VPN derived routes preferred over the backup VPN routes.
Another option (if allowed by IP addressing plan) would be the use of EIGRP summarization on VPN backup links in order to have more specific routes learned from MPLS L3 VPN PE-CE eBGP session.
To be noted if the protocol was OSPF and OSPF was also the PE-CE protocol the sham link feature allows to handle the backdoor direct link between sites.
Hope to help
Giuseppe
