I don't know about ESXi 4.1. But with ESXi 6.5, it can recognise existing VMFS (perhaps specific versions) and will ask if you want to overwrite it.
What you could do is install ESXi 5.x/6.x on a USB flash drive or SD card and boot off the hypervisor from that. You can then scan the hard disk for the existing VMFS and copy the existing VMs from it. Since you mentioned Workstation, I assume you have a copy of it. Workstation Pro can connect to ESXi hosts and there is a Download VM capability (which uses OVF Tool in the background to do so).
Recently I had a similar problem, and it was a tricky problem. Hopefully, I could place the disks on a similar server, and grab the VMDK and VMX files from the disks
Does your defective server was with a RAID hardware controller? And what kind of raid 0, 1, 5 or a more complex one? If yes then accessing the partition VMFS will be a nightmare (Maybe not in RAID1).
If you just a have one disk, then you can just connect it to a linux box through a SAStoUSB or SATAtoUSB or physically install it into the box.
Then on a Linux Debian, or Ubuntu machine, you have to install vmfs-tools package (sudo apt-get install vmfs-tools ) and mount it as read-only (sudo fdisk -l, to select the partition, then sudo vmfs-fuse /dev/your_vmfs_partition /mnt/).
Then on the folder /mnt/vmfs you should find your data.
Once that big step done you can copy the vmdk and vmx files into a new datastore.
Personally I just copied the vmdk files ( via scp) to a new Vmware vSphere server and created new VM's on it with the vmdk files as existing disks, and I also used a text editor to open the vmx files to look after the MAC addresses of the VM's and copy/paste them into the new VM's.
I hope that can help you.
Edit : Pay attention if your VM's had snapshots on it.
This is indeed possible using Workstation.
Create a Ubuntu-64 VM
Download this iso:http://sanbarrow.com/livecds/moa64-nogui/MOA64-nogui-incl-src-111014-efi.iso
Do not add a virtual disk to the VM - instead attach the original ESXi-disk via a SATA-to USB adapter.
Boot the VM from CD.
After it finished booting use the following commands:
vmfs-fuse /dev/sda3 /vmfs-readonly
Now you should be able to use WinSCP to connect to the Live Linux with user: root password:sanbarrow
If everything worked as expected you should find the VMs in /vmfs-readonly and you can copy them out.