How appalling that a menopause clinic told you that - was it a specialist clinic or a doctor/nurse at your own practice?
Regarding the thrombosis - I don't think HRT is definitely out of the question completely, but you should be referred to a specialist menopause clinic and discuss this with any specilialist you may be under for your thrombosis - if you still are.
If you look at the menopause matters website under health conditions
www.menopausematters.co.uk/atoz.php#GlossT
this is what it says about thrombosis and HRT:
"Since HRT is associated with a small increased risk of venous thrombosis, care must be taken when considering HRT use in women with a past or family history of thrombosis. Depending on the indication for HRT and on the cause of the thrombosis, risks and benefits should be assessed. If HRT is to be used, preference would usually be given to the transdermal route (patch or gel) [ref 22]. Specialist advice should be requested. Vaginal estrogen may be used for treatment of vaginal and bladder symptoms."
Here are the latest recommendations from the Brisith menopause Society and Women's health Concern paper published in May this year
min.sagepub.com/content/19/2/59.full
Venous thromboembolism (VTE) and HRT
"Oral HRT increases the risk of VTE two- to four-fold, with the highest risk in the first year of use.
VTE risk is further increased in those with a personal or family history of VTE, advanced age, obesity and other risk factors such as surgery or hospitalisation.
The VTE risk is associated with oral rather than transdermal estrogen administration and there is increasing evidence that risk is greater in combination with certain progestogens such as norpregnane derivatives and medroxyprogesterone acetate.
Individuals requiring HRT should be risk assessed and counselled regarding their VTE risk.
Routine thrombophilia testing prior to commencement on HRT is not required but testing might be considered if there is a family history of thrombosis due to a known genetic defect.
In ?high-risk? individuals who require HRT, transdermal preparations should be used and if a progestogen is required, suitable options might include micronized progesterone or dydrogesterone.
Hospitalised users of HRT require review of their therapy and should receive thromboprophylaxis as appropriate."
Hope this helps and you are able to discuss this further and maybe have a trial - because really - only oestrogen can help you.
It goes without saying you need to do everything possible to keep yourtself healthy re making sure you are not very overweight, take exercise, eat a healthy diet, do not smoke and limit alcohol....