EoIP is pretty much GRE. GRE means just slapping on another header and sending the packet merrily its way - it doesn't do anything at all for preventing reordering of packets.
You say you need an Internet connection. Is that connection going to carry more than just one connection in a layer 4 definition of the word? Have you looked at the hash methods available for 802.3ad mode?
http://wiki.mikrotik.com/wiki/Manual:In ... escription
transmit-hash-policy (layer-2 | layer-2-and-3 | layer-3-and-4; Default: layer-2) Selects the transmit hash policy to use for slave selection in balance-xor and 802.3ad modes
layer-2 - Uses XOR of hardware MAC addresses to generate the hash. This algorithm will place all traffic to a particular network peer on the same slave. This algorithm is 802.3ad compliant.
layer-2-and-3 - This policy uses a combination of layer2 and layer3 protocol information to generate the hash. Uses XOR of hardware MAC addresses and IP addresses to generate the hash. This algorithm will place all traffic to a particular network peer on the same slave. For non-IP traffic, the formula is the same as for the layer2 transmit hash policy. This policy is intended to provide a more balanced distribution of traffic than layer2 alone, especially in environments where a layer3 gateway device is required to reach most destinations. This algorithm is 802.3ad compliant.
layer-3-and-4 - This policy uses upper layer protocol information, when available, to generate the hash. This allows for traffic to a particular network peer to span multiple slaves, although a single connection will not span multiple slaves. For fragmented TCP or UDP packets and all other IP protocol traffic, the source and destination port information is omitted. For non-IP traffic, the formula is the same as for the layer2 transmit hash policy. This algorithm is not fully 802.3ad compliant.
The default is layer 2, so if you have a routed link as a point to point, all frames have the source/destination MAC addresses of the two end points and only one path each way is chosen for all traffic. But if a whole bunch of other IP traffic is routing across that link setting the modes to layer-2-and-3 or layer-3-and-4 would hash based on IP addresses or TCP/UDP ports, which would balance traffic across both links. Each connection between two end points or in the same TCP/UDP connection would still only go across one line, but overall traffic would balance. Because each connection is always on one line, you also avoid any re-ordering issues.